[Federal Register Volume 86, Number 100 (Wednesday, May 26, 2021)]
[Proposed Rules]
[Pages 28301-28323]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 2021-10421]



[[Page 28301]]

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DEPARTMENT OF COMMERCE

 Patent and Trademark Office

37 CFR Part 1

[Docket No. PTO-P-2020-0032]
RIN 0651-AD48


Electronic Submission of a Sequence Listing, a Large Table, or a 
Computer Program Listing Appendix in Patent Applications

AGENCY: United States Patent and Trademark Office, Department of 
Commerce.

ACTION: Notice of proposed rulemaking.

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SUMMARY: The United States Patent and Trademark Office (USPTO or 
Office) proposes to amend the rules of practice to permit higher-
capacity physical media to be submitted to the USPTO. Patent 
applications for certain inventions require significant data in 
American Standard Code for Information Interchange (ASCII) text format 
to be submitted to the USPTO in order to determine whether the 
invention described in the patent application is patentable. When 
submission of such data exceeds the USPTO's patent electronic filing 
system capacity, direct submission would not be possible for a large 
data submission in ASCII text format. To that end, the rules of 
practice are proposed to be amended to provide applicants with the 
ability to use physical media larger than compact discs (CDs) for 
submission of an electronic version of amino acid and nucleotide 
sequence information, information compiled in a large table, and 
information relating to a computer program listing. Additionally, 
changes regarding extraction of compressed data files, which had not 
been permitted in the past for certain submissions, would be permitted 
if compliant with the requirements of the proposed rules. Other rules 
relating to certain obsolete and non-secure methods of presenting data 
would be eliminated.

DATES: Comments must be received by July 26, 2021 to ensure 
consideration.

ADDRESSES: For reasons of Government efficiency, comments must be 
submitted through the Federal eRulemaking Portal at 
www.regulations.gov. To submit comments via www.regulations.gov, enter 
docket number PTO-P-2020-0032 on the homepage and click ``Search.'' The 
site will provide a search results page listing all documents 
associated with this docket. Find a reference to this document and 
click on the ``Comment Now!'' icon, complete the required fields, and 
enter or attach your comments. Attachments to electronic comments will 
be accepted in ADOBE[supreg] portable document format or MICROSOFT 
WORD[supreg] format. Because comments will be made available for public 
inspection, information that the submitter does not desire to make 
public, such as an address or phone number, should not be included in 
the comments.
    Visit the Federal eRulemaking Portal website (www.regulations.gov) 
for additional instructions on providing comments via the portal. If 
electronic submission of comments is not feasible due to lack of access 
to a computer and/or the internet, please contact the USPTO using the 
contact information below for special instructions.

FOR FURTHER INFORMATION CONTACT: Mary C. Till, Senior Legal Advisor, 
Office of Patent Legal Administration, Office of the Deputy 
Commissioner for Patents, by email at [email protected]; or Ali 
Salimi, Senior Legal Advisor, Office of Patent Legal Administration, 
Office of the Deputy Commissioner for Patents, by email at 
[email protected]. Contact via telephone at 571-272-7704 if further 
instruction is needed for the submission of comments.

SUPPLEMENTARY INFORMATION:
    Background: In order to permit the submission of large amounts of 
data in patent applications where such a submission exceeds the 
capacity for filing via the USPTO patent electronic filing systems, 
this rulemaking seeks to expand the types of physical media that can be 
used for such a submission. The volume of applications in which such 
large amounts of data may need to be submitted is a small fraction of 
the total number of applications that the USPTO receives every year. 
Expanding the types of physical media that can be used by these 
applicants achieves the intent with minimal changes to the USPTO's 
processing of such large amounts of data.
    With respect to the submission of data relating to biotechnology 
inventions, the proposed rules would no longer permit an applicant to 
rely on a previously submitted computer readable form (CRF) of required 
sequence information. The proposed rules thus ensure the robustness of 
the data by requiring the applicant to confirm that the data presented 
is the correct information for the examiner to consider during the 
examination process. Since the proposed rules will also permit an ASCII 
plain text file to serve as both the sequence listing itself and the 
CRF of the sequence listing, these changes are expected to have a 
minimal impact on applicants in general.
    The USPTO encourages applicants to file their patent applications 
via its USPTO patent electronic filing system and imposes a surcharge 
for non-electronic filing of an original patent application (excluding 
reissue, design, plant, and provisional applications), as mandated by 
section 10(h) of Public Law 112-29, September 16, 2011 (Leahy-Smith 
America Invents Act). The USPTO provides information (Legal Framework 
for Patent Electronic System) concerning electronic filing via the 
USPTO patent electronic filing system on its website at www.uspto.gov/patents-application-process/filing-online/legal-framework-efs-web and 
in section 502.05 of the Manual of Patent Examining Procedure (MPEP, 
Ninth Edition, Revision 10.2019). In particular, the USPTO patent 
electronic filing system permits submission of ASCII plain text files 
(.txt) for submission of a ``Sequence Listing,'' a CRF of a ``Sequence 
Listing,'' ``Large Tables,'' and a ``Computer Program Listing 
Appendix.'' Although a USPTO patent electronic filing system submission 
of such ASCII plain text files is preferred, it is possible that the 
system limitations of the USPTO patent electronic filing system may not 
accommodate large ASCII text files. Currently, in those circumstances, 
such text files may be submitted on compact disc under 37 CFR 1.52(e), 
and images of such text files may be submitted in Portable Document 
Format (PDF) via the USPTO patent electronic filing system (except for 
a CRF of a ``Sequence Listing'' or a ``Computer Program Listing 
Appendix'' having over 300 lines--these must be submitted on compact 
disc under 37 CFR 1.52(e)). The proposed changes to the rules of 
practice pertaining to a ``Sequence Listing,'' a CRF of a ``Sequence 
Listing,'' ``Large Tables,'' and a ``Computer Program Listing 
Appendix'' would harmonize the rules for filing such documents in 
electronic form with the requirements and conditions set forth in the 
Legal Framework for Patent Electronic System. The proposed changes do 
not alter the requirements and conditions set forth in the Legal 
Framework for Patent Electronic System.
    Submission of ASCII plain text files: Currently, electronic 
documents in ASCII file format that are to become part of the permanent 
USPTO records in the file of a patent application, reexamination, or 
supplemental examination proceeding that exceed the USPTO patent 
electronic filing system limits may be submitted on a compact disc. Due 
to the limited storage capacity

[[Page 28302]]

of compact discs, the USPTO is proposing revisions to permit use of 
Digital Video Disc-Recordable (DVD-R or DVD+R). These higher-capacity 
read-only optical discs, on which data is permanently recorded and 
cannot be changed or erased, significantly reduce the number of 
physical media required to accommodate large files.
    In the case of a ``Sequence Listing,'' MPEP section 2422.03 
indicates that if a new application is filed via the USPTO patent 
electronic filing system with an ASCII plain text file of a ``Sequence 
Listing'' that complies with the requirements of 37 CFR 1.824(a)(2) 
through (6) and (b), and the applicant has not filed a ``Sequence 
Listing'' in a PDF image file, the text file will serve as both the 
paper copy required by 37 CFR 1.821(c) and the CRF required by 37 CFR 
1.821(e). This concept is expressly incorporated into these proposed 
changes to the rules of practice. The current size limitation for an 
ASCII plain text file of a ``Sequence Listing'' submitted via the USPTO 
patent electronic filing system is 100 megabytes (MB). Thus, if an 
applicant files an ASCII plain text file of a ``Sequence Listing'' that 
is 100 MB or less, that ASCII plain text file serves as both the 
``Sequence Listing'' under 37 CFR 1.821(c) and the CRF of the 
``Sequence Listing'' under 37 CFR 1.821(e). With respect to ``Large 
Tables'' and a ``Computer Program Listing Appendix,'' if ASCII plain 
text files are filed through the USPTO patent electronic filing system, 
then no separate submission of disc copies of ASCII plain text files 
are needed. However, the current system limit of ASCII plain text file 
submissions of ``Large Tables'' and a ``Computer Program Listing 
Appendix'' is 25 MB per submission. This limit, however, may not 
prevent an entirely electronic submission. According to the Legal 
Framework for Patent Electronic System, cited supra, a user may be able 
to break up a ``Computer Program Listing Appendix'' or ``Large Tables'' 
file that is larger than 25 MB into multiple files that are no larger 
than 25 MB each and submit those smaller files via the USPTO patent 
electronic filing system. If the user chooses to break up a large 
``Computer Program Listing Appendix'' or ``Large Tables'' file so it 
may be submitted electronically, the file names must indicate their 
order (e.g., ``1 of X,'' ``2 of X''). Files above the 25 MB limit for 
``Large Tables'' and a ``Computer Program Listing Appendix'' (unless 
capable of being divided) and above 100 MB for a ``Sequence Listing'' 
will have to be submitted on read-only optical discs. Submission of a 
``Sequence Listing'' as an ASCII text file, if it exceeds 100 MB, 
cannot be divided like a submission of a ``Large Table'' or a 
``Computer Program Listing Appendix.'' Thus, any ``Sequence Listing'' 
greater than 100 MB must be submitted on read-only optical discs. 
Currently, such files cannot be compressed; this can necessitate the 
use of multiple CD-ROMs or CD-Rs. These proposed changes to the rules 
of practice will permit higher-capacity media as well as non-self-
extracting file compression. By permitting file compression, material 
submitted on a read-only optical disc will be capable of fitting on a 
single disc with the data integrity remaining intact.
    The current rules of practice (37 CFR 1.52(e), 1.96(c), and 1.824) 
recite the use of certain obsolete computer and operating system 
formats. Updated computer and operating system formats are proposed to 
be added, and reference to obsolete media will be eliminated. Proposed 
changes to 37 CFR 1.58 will recite the updated computer and operating 
system compatibilities.
    When a patent application relies on subject matter from an ASCII 
plain text file submitted on physical media or via the USPTO patent 
electronic filing system, currently, the patent specification must 
contain an incorporation by reference statement pursuant to 37 CFR 
1.77(b)(5) or the Legal Framework for Patent Electronic System. The 
rules relating to the arrangement of the specification are proposed to 
be amended to clarify the required incorporation by reference 
statement. The granted patent or pre-grant publication of an 
application that includes an ASCII plain text file, whether submitted 
on optical read-only discs or via the USPTO patent electronic filing 
system, does not include the actual contents of the ASCII plain text 
file in the printed document. The incorporation by reference is 
necessary to treat the material in the ASCII file as part of the patent 
or publication and to alert the public that the granted patent or the 
pre-grant publication includes additional material that constitutes 
part of the patent or publication. Although the current rules and 
proposed changes to the rules of practice permit a cross-reference to 
related applications to be included in the specification, in accordance 
with 37 CFR 1.76, it should be noted that the USPTO does not recognize 
a benefit or priority claim presented only in the specification for 
patent applications filed on or after September 16, 2012. For these 
applications or patents issued from such applications, a benefit claim 
(37 CFR 1.78) or priority claim (37 CFR 1.55) must be presented on an 
Application Data Sheet for an original application in order to be 
recognized by the USPTO.
    Sequence Listings: Any patent application that contains unbranched 
nucleotide sequences with 10 or more nucleotide bases or unbranched, 
non-D amino acid sequences with 4 or more amino acids, provided that 
there are at least 10 ``specifically defined'' nucleotides or 4 
``specifically defined'' amino acids, must contain a ``Sequence 
Listing'' and a CRF of the ``Sequence Listing.'' Under the current 
rules, a ``Sequence Listing'' exceeding the USPTO patent electronic 
filing system submission limit must be submitted with a total of three 
disc copies to the USPTO to comply with the ``Sequence Listing'' 
regulation requirements. The three disc copies are (1) a first disc 
copy of ASCII plain text file on a compact disc to comply with 37 CFR 
1.821(c), (2) a second identical disc copy of the ASCII plain text file 
on compact disc to comply with the duplicate submission requirement in 
37 CFR 1.52(e)(4) when submitting the 37 CFR 1.821(c) sequence listing, 
and (3) a CRF copy of the ASCII plain text file on compact disc, 
identical to the 37 CFR 1.821(c) submission. The proposed rule changes 
would permit that a single read-only optical disc copy of a ``Sequence 
Listing'' as an ASCII plain text file could be submitted, and that such 
submission would comply with both the listing requirement (37 CFR 
1.821(c)) and the CRF requirement (37 CFR 1.821(e)). For submission via 
the USPTO patent electronic filing system, the ASCII plain text file, 
not the PDF version, would serve to comply with both 37 CFR 1.821(c) 
and 1.821(e). The following table summarizes the mechanics of 
submitting a ``Sequence Listing'' under the proposed changes to the 
rules of practice in applications, except for international 
applications during the international stage, based on the current USPTO 
patent electronic filing system limit of 100 MB for an ASCII plain text 
file and a system limit of 25 MB for PDF files.

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                                                                                              Surcharge under 37
                                                                                                CFR 1.21(o) for
                                       Preferred          Acceptable         Specification      submission of a
  Size of ``Sequence Listing''        submission          submission           statement          ``Sequence
                                                                             requirements        Listing'' in
                                                                                                electronic form
----------------------------------------------------------------------------------------------------------------
100 MB or less..................  ASCII plain text    The ``Sequence      Incorporation by    None.
                                   file submitted      Listing'' in        reference of the
                                   via the USPTO       physical paper      ASCII text file
                                   patent electronic   copies or           into the
                                   filing system,      submitted via the   specification
                                   complies with       USPTO patent        (see MPEP 502.05).
                                   both 37 CFR         electronic filing
                                   1.821(c) and        system as a PDF
                                   1.821(e), no        image file and a
                                   separate CRF        CRF on a read-
                                   needed.             only optical disc
                                                       along with a
                                                       statement that
                                                       the CRF and the
                                                       physical paper/
                                                       PDF image file
                                                       submission are
                                                       the same.
101 MB to 299 MB................  ASCII plain text    The ``Sequence      Incorporation by    None.
                                   file submitted on   Listing'' in        reference of the
                                   a read-only         physical paper      ASCII text file
                                   optical disc in a   copies and a CRF    into the
                                   single copy, the    on a read-only      specification (37
                                   single copy         optical disc        CFR 1.52(e)(8)).
                                   complies with       along with a
                                   both 37 CFR         statement that
                                   1.821(c) and        the CRF and the
                                   1.821(e), no        physical paper
                                   separate CRF        submission are
                                   needed.             the same.
300 MB to 799 MB................  ASCII plain text    The ``Sequence      Incorporation by    37 CFR 1.21(o)(1):
                                   file submitted on   Listing'' in        reference of the    Currently $1,000
                                   a read-only         physical paper      ASCII text file     for an
                                   optical disc in a   copies and a CRF    into the            undiscounted
                                   single copy, the    on a read-only      specification (37   entity, $500 for
                                   single copy         optical disc        CFR 1.52(e)(8)).    a small entity,
                                   complies with       along with                              and $250 for a
                                   both 37 CFR         statement that                          micro entity.
                                   1.821(c) and        the CRF and the
                                   1.821(e), no        physical paper
                                   separate CRF        submission are
                                   needed.             the same.
800 MB or above.................  ASCII plain text    The ``Sequence      Incorporation by    37 CFR 1.21(o)(2):
                                   file submitted on   Listing'' in        reference of the    Currently $10,000
                                   a read-only         physical paper      ASCII text file     for an
                                   optical disc in a   copies and a CRF    into the            undiscounted
                                   single copy, the    on a read-only      specification (37   entity, $5,000
                                   single copy         optical disc        CFR 1.52(e)(8) as   for a small
                                   complies with       along with a        added in these      entity, and
                                   both 37 CFR         statement that      proposed rules).    $2,500 for a
                                   1.821(c) and        the CRF and the                         micro entity.
                                   1.821(e), no        physical paper
                                   separate CRF        submission are
                                   needed. Should      the same.
                                   more than one
                                   disc be needed,
                                   then only a
                                   single copy of
                                   the additional
                                   disc(s) would be
                                   needed, no
                                   additional CRF
                                   needed since the
                                   read-only optical
                                   discs (if
                                   multiple are
                                   needed) need NOT
                                   be submitted in
                                   duplicate.
----------------------------------------------------------------------------------------------------------------

    The current rules of practice relating to form, content, and 
submission requirements of ``Sequence Listings'' comply with World 
Intellectual Property Organization (WIPO) Standard ST.25. In this 
document, the proposed rule changes and modifications also conform to 
WIPO Standard ST.25.
    To simplify and streamline the processing of patent applications 
with sequences of amino acids and nucleotides as defined in 37 CFR 
1.821(a), submission of a ``Sequence Listing'' in ASCII plain text file 
format, either directly via the USPTO patent electronic filing system 
or on a read-only optical disc, will be sufficient to comply with the 
listing requirement and the CRF requirement (37 CFR 1.821(c) and 
1.821(e)). That is, if a ``Sequence Listing'' in ASCII plain text file 
format is filed either directly via the USPTO patent electronic filing 
system or on a read-only optical disc, then no additional CRF copy will 
be needed. In such a situation, an incorporation by reference statement 
in the specification, in accordance with 37 CFR 1.77(b)(5), would still 
be required, except such a statement will not be required in an 
international application during the international stage. As with the 
current rules, the proposed changes continue to permit submission of a 
``Sequence Listing'' on physical sheets of paper or as a PDF image 
file. Furthermore, like the current rules, the proposed rules will 
require payment of the application size fee (37 CFR 1.16(s)) for 
physical sheets of paper of a ``Sequence Listing'' or a PDF of a 
``Sequence Listing'' that results in an application size that exceeds 
100 sheets of paper. Submission of the ``Sequence Listing'' as a PDF or 
on physical sheets of paper would still require a separate CRF of the 
``Sequence Listing.'' Similarly, should the ASCII plain text file of 
the ``Sequence Listing'' exceed the system limits of the USPTO patent 
electronic filing system (currently at 100 MB), then a single copy of 
an ASCII plain text file of the ``Sequence Listing'' submitted on a 
read-only optical disc would not require a separate electronic copy of 
a CRF of the ``Sequence Listing.'' In circumstances in which a separate 
CRF is filed, the statement, in accordance with 37 CFR 
1.821(e)(2)(iii), that the CRF is identical to either the PDF or the 
physical paper version of the ``Sequence Listing'' is required.
    The proposed rule changes will no longer permit the transfer of a 
CRF from a parent or related application to the newly filed original 
application. In light of the availability to download a ``Sequence 
Listing'' from granted U.S. patents and U.S. patent application 
publications via Public PAIR in the Supplemental Content tab, there is 
no longer a need for a CRF transfer. Such electronic copies of a 
``Sequence Listing'' may also be available on another intellectual 
property office's website or on the WIPO--PATENTSCOPE website. In the 
extremely rare circumstance in which the ``Sequence Listing'' exceeds 
the download capability (currently 650 MB), then a request for the 
content of a granted U.S. patent or U.S. patent application publication 
(including the ``Sequence Listing'' submitted on disc) can be made to 
the Patent and Trademark Copy Fulfillment Branch. Therefore, these 
proposed changes to the rules of practice will eliminate the practice 
of CRF transfers.
    WIPO Standard ST.26 is expected to take effect on January 1, 2022, 
and will replace WIPO Standard ST.25. WIPO Standard ST.26 will require 
that a

[[Page 28304]]

``Sequence Listing'' must be presented as a single file in eXtensible 
Markup Language (XML). As a result, in an original application filed on 
or after January 1, 2022, the ``Sequence Listing'' part will not be 
accepted on physical sheets of paper or as a PDF image file. Therefore, 
to prepare for the changes under WIPO Standard ST.26, the USPTO is 
proposing to revise the rules of practice to facilitate ``Sequence 
Listing'' submissions by requiring a single ASCII plain text file 
submission that would both meet the ``Sequence Listing'' requirement 
and serve as the CRF of the ``Sequence Listing.'' That is, under these 
proposed rule changes, a single ASCII plain text file submission of a 
``Sequence Listing'' would comply with both 37 CFR 1.821(c) and (e).
    Currently, 37 CFR 1.821(a) incorporates by reference six tables 
from Appendix 2 of WIPO Standard ST.25 that provide the nucleotide and 
amino acid symbols and feature tables. For convenience, a further 
proposed modification of the ``Sequence Listing'' rules involves adding 
these tables as Appendices A-F of Subpart G of Part 1 (explicitly 
incorporating the text of the WIPO tables into the CFR). Currently, 37 
CFR 1.823(b) includes a table containing all numeric identifiers. To 
improve the readability of the regulations, this table is proposed to 
be moved to Appendix G.
    Updates to amendment practice for ``Large Tables,'' a ``Computer 
Program Listing Appendix,'' and ``Sequence Listings'': In general, the 
manner of making amendments in applications requires that the text of 
any added subject matter must be shown by underlining the added text 
and that the text of any deleted matter must be shown by strike-
through. However, computer listings (37 CFR 1.96) and ``Sequence 
Listings'' (37 CFR 1.825) are currently exempted from these general 
requirements (37 CFR 1.121(b)). These proposed changes to the rules of 
practice will require a description of the amendments made in ``Large 
Tables,'' a ``Computer Program Listing Appendix,'' and ``Sequence 
Listings'' to more easily and accurately identify any changes made to 
the information contained in such submissions (37 CFR 1.121(b)(6)).
    This proposed rule includes requirements for amendments to an ASCII 
plain text file containing ``Large Tables'' (37 CFR 1.58(g)) or a 
``Computer Program Listing Appendix'' (37 CFR 1.96(c)(5)(i)) that are 
accomplished by a replacement of an ASCII plain text file. Providing a 
replacement may be required if, for example, the information on the 
disc is corrupted. A replacement ASCII plain text file must be 
submitted, either via the USPTO patent electronic filing system or on a 
read-only optical disc, together with an incorporation by reference of 
the material in the replacement ASCII plain text file in a separate 
paragraph of the specification; a statement that identifies the 
location of all deletions, replacements, or additions to the ASCII 
plain text file; and a statement that the replacement ASCII plain text 
file contains no new matter.

Discussion of Specific Rules

    Section 1.52: The heading of Sec.  1.52 is proposed to read: 
Language, paper, writing, margins, read-only optical disc 
specifications.
    Section 1.52(e) is proposed to be amended to reference electronic 
documents ``submitted on a read-only optical disc,'' with additional 
conforming changes made throughout. Currently, Sec.  1.52(e) references 
``electronic documents'' that are to become part of the USPTO records 
in patent applications, reexaminations, and supplemental examination 
proceedings. Since Sec.  1.52(e) only governs electronic documents 
submitted on discs, in particular as proposed, read-only optical discs, 
the heading is more specific to the types of electronic documents 
covered by the regulation.
    Section 1.52(e)(1) is proposed to be updated to specifically refer 
to a ``Computer Program Listing Appendix,'' as provided for in Sec.  
1.96(c), and to require that the ``Sequence Listing'' on a read-only 
optical disc submitted under Sec.  1.821(c) must be in compliance with 
Sec.  1.824. Section 1.52(e)(1) is proposed to be revised to indicate 
that ``Large Tables,'' as described in the proposed changes to Sec.  
1.58(c), may be submitted on a read-only optical disc to become part of 
the permanent USPTO record.
    Section 1.52(e)(2) is proposed to be revised to replace ``compact'' 
with ``read-only optical'' and to incorporate conformity to the 
International Organization for Standardization (ISO) 9660 standard, 
which was previously located in Sec.  1.52(e)(3). Additionally, Sec.  
1.52(e)(2) maintains the availability of CD-ROM and CD-R as options for 
physical media (Sec.  1.52(e)(2)(i)) but also expands the types of 
media options to include Digital Video Disc-Recordable (DVD-R or DVD+R) 
(Sec.  1.52(e)(2)(ii)).
    Section 1.52(e)(3) is proposed to be reorganized for improved 
readability. The computer compatibility (Sec.  1.52(e)(3)(i)) and 
operating system compatibility (Sec.  1.52(e)(3)(ii)) are expressly 
provided. Furthermore, the proposed changes to the rules of practice 
indicate the use of ASCII plain text is required when submitting files 
on physical media (Sec.  1.52(e)(3)(iii)). The proposed changes would 
permit file compression for ASCII plain text files, which must be done 
in accordance with Sec. Sec.  1.58, 1.96, and 1.824, as applicable 
(Sec.  1.52(e)(3)(iii)).
    Section 1.52(e)(4) is proposed to be revised to eliminate its 
requirements for a duplicate copy and accompanying statement that the 
two discs are identical. References to ``Copy 1'' and ``Copy 2'' are 
deleted, and references to ``compact disc'' are updated to ``read-only 
optical disc.'' However, duplicate copies of read-only optical discs 
for ``Large Tables'' or a ``Computer Program Listing Appendix'' will 
still be required, and Sec. Sec.  1.58 and 1.96 are proposed to be 
amended to provide for such duplicate copies. Duplicate copies for 
``Large Tables'' and a ``Computer Program Listing Appendix'' would 
still be required to be submitted since the Office of Patent 
Application Processing (OPAP) keeps a first copy for record retention 
purposes and a second copy in an artifact folder for use by the 
examiner during the patent examination process. A ``Sequence Listing,'' 
however, is not processed in the same manner. Accordingly, only a 
single copy of a read-only optical disc containing the ``Sequence 
Listing'' in ASCII plain text is needed, as such copy will serve as 
both the listing as required by 37 CFR 1.821(c) and the CRF copy as 
required by 37 CFR 1.821(e). Section 1.52(e)(4) is also proposed to 
require that the read-only optical discs are enclosed in a hard case 
within an unsealed, padded, and protective mailing envelope and that 
such submission is accompanied by a transmittal letter. The information 
regarding the read-only optical disc to be included in the transmittal 
letter is expressly enumerated in items (i)-(vi) of this rule.
    Section 1.52(e)(5) is proposed to be revised to enumerate the 
labeling requirements of the read-only optical disc that had previously 
been enumerated in Sec.  1.52(e)(6). The incorporation by reference 
found in the current Sec.  1.52(e)(5) is deleted and moved to Sec.  
1.52(e)(8).
    Section 1.52(e)(6) is proposed to be revised to state that the 
read-only optical discs may not be retained as part of the patent 
application file and will not be returned to the applicant. The current 
USPTO processing of compact discs would equally apply to read-only 
optical discs. For ``Large Tables'' or a ``Computer Program Listing 
Appendix,'' the process involves the OPAP receiving the read-only 
optical discs, creating an artifact sheet for inclusion in the Image 
File Wrapper, and reviewing the ASCII plain text file. Under the 
current rules, a first copy of the read-only optical disc

[[Page 28305]]

is kept for record retention purposes, and a second copy is maintained 
in an artifact folder for use by the examiner during the patent 
examination process. For a ``Sequence Listing,'' the proposal would 
require the submission of a single read-only optical disc. Once the 
``Sequence Listing'' is loaded into the USPTO's Supplemental Complex 
Repository for Examiners (SCORE) system, the physical media may be 
retained by the Patent Legal Research Center. A ``Sequence Listing'' 
from granted U.S. patents and U.S. patent application publications is 
available via Public PAIR in the Supplemental Content tab. Such 
electronic copies of a ``Sequence Listing'' may also be available on 
another intellectual property office's website, or on the WIPO--
PATENTSCOPE website. In the extremely rare circumstance in which the 
``Sequence Listing'' exceeds the download capability (currently 650 
MB), then a request for the content of a granted U.S. Patent or U.S. 
patent application publication (including the ``Sequence Listing'' 
submitted on disc) can be made to the Patent and Trademark Copy 
Fulfillment Branch.
    Section 1.52(e)(7) is proposed to be revised to state that any 
amendment to the information on a read-only optical disc must be made 
in accordance with specified provisions, specifically, in compliance 
with Sec.  1.58(g) for ``Large Tables,'' Sec.  1.96(c)(5) for a 
``Computer Program Listing Appendix,'' and Sec.  1.825(b) for a 
``Sequence Listing'' or a CRF of a ``Sequence Listing.''
    Section 1.52(e)(8) is proposed to be added to state that the 
specification must contain an incorporation by reference (Sec.  
1.77(b)(5)) of the material contained on each read-only optical disc in 
a separate paragraph, except for an international application in the 
international stage. Additionally, the USPTO may require the applicant 
to amend the specification to include the material incorporated by 
reference.
    Section 1.52(e)(9) is proposed to be added to indicate that should 
a file be unreadable, then the USPTO will treat the submission as not 
ever having been submitted. A file is unreadable if, for example, it is 
of a format that does not comply with the requirements of Sec.  
1.52(e)(2), it is corrupted, or it is written onto a defective read-
only optical disc. In such a case, OPAP will issue a notice indicating 
that the file is unreadable, and a replacement will be required.
    Section 1.52(f) is proposed to be amended to include the subtitle 
``Determining application size fees for applications containing 
electronic documents submitted on a read-only optical disc or via the 
USPTO patent electronic filing system.''
    Section 1.52(f)(1) is proposed to be amended to clarify the 
determination of application size fees for application components 
submitted on a read-only optical disc in compliance with Sec.  1.52(e), 
where an electronic form of any ``Sequence Listing,'' in compliance 
with either Sec.  1.821(c) or (e), and any ``Computer Program Listing 
Appendix,'' in compliance with Sec.  1.96(c), are specifically excluded 
from the application size fee determination. As stated in 35 U.S.C. 
41(a)(1)(G), ``any sequence listing'' or a ``computer program listing'' 
submitted in electronic form is expressly excluded from any application 
size fee calculation. A ``Computer Program Listing Appendix'' is 
considered a ``computer program listing.''
    Section 1.52(f)(2) is proposed to be amended to clarify the 
determination of application size fees for applications submitted in 
whole or in part via the USPTO patent electronic filing system and also 
to clarify that any electronic form of a ``Sequence Listing,'' in 
compliance with either Sec.  1.821(c) or (e), and any ``Computer 
Program Listing Appendix,'' in compliance with Sec.  1.96(c), are 
specifically excluded from the application size fee determination. As 
stated in 35 U.S.C. 41(a)(1)(G), ``any sequence listing'' or a 
``computer program listing'' submitted in electronic form is expressly 
excluded from any application size fee calculation. A ``Computer 
Program Listing Appendix'' is considered a ``computer program 
listing.''
    Section 1.52(f)(3) is proposed to be added to provide a surcharge 
for submission of a ``Sequence Listing'' in electronic form in an 
application under 35 U.S.C. 111 or 371 that is 300 MB or larger in 
size. The lengthy ``Sequence Listing'' surcharge is set forth in Sec.  
1.21(o). This means that a ``Sequence Listing'' submitted in electronic 
form on read-only optical discs in compliance with either Sec. Sec.  
1.821(c) either/or 1.821(e) that is 300 MB or larger in size will incur 
a surcharge under Sec.  1.21(o). When the electronic form of the 
``Sequence Listing'' is between 300 MB and 800 MB, a surcharge under 
Sec.  1.21(o)(1) will be required. If the electronic form of the 
``Sequence Listing'' exceeds 800 MB, then a surcharge under Sec.  
1.21(o)(2) will be imposed.
    Section 1.58: Section 1.58(b) is proposed to delete references to 
Sec. Sec.  1.96(c) and 1.821(c) regarding tables submitted in 
electronic form and to set forth format requirements, from former Sec.  
1.58(c), that apply generally to chemical and mathematical formulas and 
tables.
    Section 1.58(c) is proposed to be rewritten to define ``Large 
Tables'' that may be submitted in electronic form in ASCII plain text 
via the USPTO patent electronic filing system or on a read-only optical 
disc, in compliance with Sec.  1.52(e), excluding an international 
application during the international stage. Additionally, the current 
USPTO processing of ``Large Tables'' submitted on a read-only optical 
disc involves a first copy, for record retention purposes, and a second 
copy, for use during the examination process.
    Section 1.58(d) is proposed to be added to list the format 
requirements of ``Large Tables'' submitted in electronic form in ASCII 
plain text. The format requirements address the spatial relationship of 
table elements, computer compatibility, operating system compatibility, 
the use of ASCII plain text, the naming conventions for the .txt file, 
and an incorporation by reference statement to be included in the 
specification, as per Sec.  1.77(b)(5).
    Section 1.58(e) is proposed to be added to state that ``Large 
Tables'' submitted via the USPTO patent electronic filing system must 
not exceed 25 MB, and file compression is not permitted. It is noted 
that when submitting via the USPTO patent electronic filing system, it 
is possible to submit multiple files that are 25 MB or less in size, as 
per the Legal Framework for Patent Electronic System cited supra.
    Section 1.58(f) is proposed to be added to specify the technical 
requirements for ``Large Tables'' submitted on read-only optical discs 
in compliance with Sec.  1.52(e) and that compression is permitted. 
Section 1.58(f) also specifies the permitted manner of file 
compression.
    Section 1.58(g) is proposed to be added to provide the procedure 
that would be applicable should an amendment of one or more ``Large 
Tables'' be required. If an amendment is required to be made to a 
``Large Table,'' then a replacement submission via the USPTO patent 
electronic filing system or on duplicate read-only optical discs would 
be necessary. An updated incorporation by reference statement would be 
required along with the necessary statement regarding any deletions, 
replacements or addition to the ASCII plain text file and a statement 
that the replacement ASCII plain text file contains no new matter.
    Section 1.58(h) is proposed to be added to specify that should 
``Large Tables'' be submitted as an ASCII plain text file on the 
application filing date,

[[Page 28306]]

but no incorporation by reference of the material contained therein has 
been made, an amendment containing a separate paragraph incorporating 
by reference the material contained in the ASCII plain text file, as 
per Sec.  1.77(b)(5), will be required.
    Section 1.58(i) is proposed to be added to require that any read-
only optical disc for a ``Large Table'' be submitted in duplicate. 
Section 1.58(i) sets forth the criteria for labeling and necessary 
statements as to the identity of the read-only optical discs. This 
section indicates how the USPTO will treat the submission of the two 
read-only optical discs that are not identical to each other. Duplicate 
copies for ``Large Tables'' are required to be submitted since the OPAP 
keeps a first copy for record retention purposes and a second copy in 
an artifact folder for use by the examiner during the patent 
examination process.
    Section 1.58(j) is proposed to be added to require that any 
amendment to the information on a read-only optical disc must be by way 
of a replacement read-only optical disc, in compliance with Sec.  
1.58(g), where the replacement read-only optical disc and copy must be 
labeled ``COPY 1 REPLACEMENT MM/DD/YYYY'' (with the month, day, and 
year of creation indicated) and ``COPY 2 REPLACEMENT MM/DD/YYYY,'' 
respectively. This section indicates how the USPTO will treat the 
submission of the two replacement read-only optical discs that are not 
identical to each other.
    Section 1.71: Section 1.71(f) is proposed to be revised to clarify 
that a ``Sequence Listing,'' if required or submitted under Sec.  
1.821(c), should be submitted on a separate sheet. This is directed to 
those submissions of the ``Sequence Listing'' submitted on physical 
sheets of paper or submitted as a PDF image file via the USPTO patent 
electronic filing system. In such cases where there is a separate 
``Sequence Listing'' and a separate CRF of the ``Sequence Listing,'' 
the ``Sequence Listing'' must be on a separate sheet(s).
    Section 1.77: Section 1.77(b)(5) is proposed to be revised to 
clarify when an incorporation by reference is needed. The proposed rule 
change provides for incorporation by reference of ASCII plain text 
files submitted via the USPTO patent electronic filing system or on one 
or more read-only optical discs for a ``Computer Program Listing 
Appendix,'' a ``Sequence Listing,'' or ``Large Tables,'' as provided 
for in Sec. Sec.  1.96(c), 1.821(c), or 1.58(c), respectively. The 
proposed incorporation by reference statement would identify the names 
of each ASCII plain text file and specify, if applicable, the files 
contained on each of the read-only optical discs, their dates of 
creation, and the sizes of each ASCII plain text file in bytes.
    Section 1.77(b)(13) is proposed to be revised to clarify that the 
``Sequence Listing'' required by Sec.  1.821(c), submitted on physical 
sheets of paper or as a PDF image file of the ``Sequence Listing,'' 
should follow the other sections of the specification.
    Section 1.96: Section 1.96(a) is proposed to be revised to replace 
``printout'' with ``document.''
    Section 1.96(c) is proposed to be revised to set forth the 
requirements that apply to any ``Computer Program Listing Appendix'' 
that will not be part of the printed patent specification. The appendix 
must be submitted as an electronic document in ASCII plain text, 
whether submitted via the USPTO patent electronic filing system or on a 
read-only optical disc, in compliance with Sec.  1.52(e). Proposed 
requirements for the ``Computer Program Listing Appendix'' include that 
it must be incorporated by reference in the specification, as set forth 
in Sec.  1.77(b)(5), and have certain computer compatibilities (Sec.  
1.96(c)(1)), naming convention adherences (Sec.  1.96(c)(2)), and size 
limitations (Sec.  1.96(c)(3)).
    Section 1.96(c)(4) is proposed to be added to state requirements 
(i) through (vi) where the ``Computer Program Listing Appendix'' is 
submitted on a read-only optical disc, in compliance with Sec.  
1.52(e).
    Section 1.96(c)(5) is proposed to be added to state requirements 
(i) through (iv) for amendments to delete, replace, or add to the 
information of a ``Computer Program Listing Appendix'' submitted in 
electronic form in ASCII plain text.
    Section 1.96(c)(6) is proposed to be added to indicate that should 
a ``Computer Program Listing Appendix'' be present on the filing date 
of the application without an express incorporation by reference in the 
specification relating to the material contained in the ASCII plain 
text file, in accordance with Sec.  1.77(b)(5), then an amendment to 
include such a paragraph in the specification will be required.
    Section 1.96(c)(7) is proposed to be added to indicate that a 
submission of a ``Computer Program Listing Appendix'' on a read-only 
optical disc must be completed in duplicate, since the processing by 
the USPTO of a ``Computer Program Listing Appendix'' submitted on a 
read-only optical disc involves keeping a first copy for record 
retention purposes and using a second copy during the examination 
process. The new section sets forth the criteria for labeling and 
necessary statements as to the identity of the read-only optical discs. 
This proposed section indicates how the USPTO will treat the submission 
of the two read-only optical discs should they not be identical.
    Section 1.121: Section 1.121(b) is proposed to be revised, and 
Sec.  1.121(b)(6) is proposed to be added, to clarify that ``Large 
Tables'' in accordance with Sec.  1.58(c), a ``Computer Program Listing 
Appendix'' in accordance with Sec.  1.96(c)(5) and (7), and a 
``Sequence Listing'' or CRF in accordance with Sec.  1.825 must be 
amended in accordance with Sec.  1.58(g), Sec.  1.96(c)(5), and Sec.  
1.825, respectively.
    Section 1.173: The heading of Sec.  1.173(b)(1) is proposed to be 
revised to reflect that, in a reissue application, changes to the 
claims, ``Large Tables'' (Sec.  1.58(c)), a ``Computer Program Listing 
Appendix'' (Sec.  1.96(c)), or a ``Sequence Listing'' (Sec.  1.821(c)) 
are made in a different manner from changes to other parts of the 
specification.
    The manner of making changes to the specification, other than to 
the claims, set forth in current Sec.  1.173(b)(1) is proposed to be 
moved to new Sec.  1.173(b)(1)(i). New Sec.  1.173(b)(1)(i) specifies 
that it does not apply to changes to ``Large Tables'' (Sec.  1.58(c)), 
a ``Computer Program Listing Appendix'' (Sec.  1.96(c)), or a 
``Sequence Listing'' (Sec.  1.821(c)), in addition to not applying to 
changes to the claims. Additionally, the language from current Sec.  
1.173(b)(1) stating that the paragraph is not applicable to discs is 
proposed to not be included in new Sec.  1.173(b)(1)(i).
    Section Sec.  1.173(b)(1)(ii) is proposed to be added to specify 
that changes to ``Large Tables,'' a ``Computer Program Listing 
Appendix,'' or a ``Sequence Listing'' must be made in accordance with 
Sec.  1.58(g) for ``Large Tables,'' Sec.  1.96(c)(5) for a ``Computer 
Program Listing Appendix,'' and Sec.  1.825 for a ``Sequence Listing.''
    Section 1.173(d) is proposed to be revised to exclude changes to 
``Large Tables,'' a ``Computer Program Listing Appendix,'' or a 
``Sequence Listing'' from the changes that must be shown by markings in 
a reissue application.
    Section Sec.  1.173(d)(2) is proposed to be revised to delete the 
following: ``except for amendments submitted on compact discs 
(Sec. Sec.  1.96 and 1.821(c)). Matter added by reissue on compact 
discs must be preceded with `' and end with `' to properly 
identify the material being added.''
    Section 1.530: The heading of Sec.  1.530(d)(1) is proposed to be 
revised to reflect that, in a reexamination proceeding, changes to the 
claims, ``Large Tables'' (Sec.  1.58(c)), a ``Computer Program Listing 
Appendix'' (Sec.  1.96(c)),

[[Page 28307]]

and a ``Sequence Listing'' (Sec.  1.821(c)) are made in a different 
manner from changes to the other parts of the specification.
    The manner of making changes to the specification, other than to 
the claims, set forth in current Sec.  1.530(d)(1) is proposed to be 
moved to new Sec.  1.530(d)(1)(i). New Sec.  1.530(d)(1)(i) specifies 
that it does not apply to changes to ``Large Tables'' (Sec.  1.58(c)), 
a ``Computer Program Listing Appendix'' (Sec.  1.96(c)), and a 
``Sequence Listing'' (Sec.  1.821(c)), in addition to not applying to 
changes to the claims.
    Section 1.530(d)(1)(ii) is proposed to be added to specify that 
changes to ``Large Tables,'' a ``Computer Program Listing Appendix,'' 
or a ``Sequence Listing'' must be made in accordance with Sec.  1.58(g) 
for ``Large Tables,'' Sec.  1.96(c)(5) for a ``Computer Program Listing 
Appendix,'' and Sec.  1.825 for a ``Sequence Listing.''
    Section 1.821: Section 1.821(a) is proposed to be revised to remove 
all prior references to WIPO Standard ST.25 (1998) and instead cross-
reference new Appendices A through F to part 1 of 37 CFR, subpart G, 
which would contain the updated 2009 version of the tables from WIPO 
Standard ST.25.
    Section 1.821(c) is proposed to be revised to delete references to 
a paper or compact disc copy (Sec.  1.52(e)), delete discussion of 
sequence identifiers, and indicate that the criteria for submission of 
a ``Sequence Listing,'' except for national stage entry under Sec.  
1.495(b)(1), is set forth in newly proposed Sec.  1.821(c)(1)-(3). 
Information about sequence identifiers has been moved to Sec.  
1.823(a).
    Section 1.821(c)(1) is proposed to be added to require that the 
``Sequence Listing'' can be submitted as an ASCII plain text file via 
the USPTO patent electronic filing system or on a read-only optical 
disc copy, where the form and format of the ``Sequence Listing'' 
conforms to Sec.  1.824 and an incorporation by reference statement as 
required by Sec.  1.52(e) is provided. Section 1.821(c)(2) is proposed 
to be added to permit submission of a ``Sequence Listing'' as a PDF 
file via the USPTO patent electronic filing system. Section 1.821(c)(3) 
is proposed to be added to permit the submission of a ``Sequence 
Listing'' on physical sheets of paper.
    Section 1.821(d) is proposed to be revised to add that where a 
sequence is presented in a drawing, reference must be made to the 
sequence by use of a sequence identifier, either in the drawing or in 
the Brief Description of the Drawings, where the correlation between 
multiple sequences in the drawing and their sequence identifiers in the 
Brief Description is clear. A sequence found in a drawing sheet is not 
a ``Sequence Listing'' under Sec.  1.821(c) or (e). Therefore, a 
separate ``Sequence Listing'' would be required to comply with Sec.  
1.821(c). If the ``Sequence Listing'' was submitted as a PDF image file 
via the USPTO patent electronic filing system or on physical sheets of 
paper, a separate CRF of the ``Sequence Listing'' would be required to 
comply with Sec.  1.821(e).
    Section 1.821(e)(1) is proposed to be added to set forth the 
requirements in Sec.  1.821(e)(1)(i) for submission of a CRF of the 
``Sequence Listing,'' in compliance with Sec.  1.824, when a ``Sequence 
Listing'' was submitted as a PDF image file via the USPTO patent 
electronic filing system or on physical sheets of paper for an 
application filed under 35 U.S.C. 111(a). The proposed rule (Sec.  
1.821(e)(1)(ii)) also indicates that a statement is required to confirm 
that the CRF is identical to the ``Sequence Listing'' under Sec.  
1.821(c), when the submission of the ``Sequence Listing'' under Sec.  
1.821(c) was on physical sheets of paper or as a PDF image file via the 
USPTO patent electronic filing system.
    Section 1.821(e)(2) is proposed to be added to set forth the 
requirements where the ``Sequence Listing'' under Sec.  1.821(c) in an 
application submitted under 35 U.S.C. 371 is in a PDF file (Sec.  
1.821(c)(2)) or on physical sheets of paper (Sec.  1.821(c)(3)), and 
not also as an ASCII plain text file, in compliance with Sec.  1.824 
(Sec.  1.821(c)(1)). In such situations, the following are required: 
(1) A copy of the ``Sequence Listing'' in CRF, in accordance with the 
requirements of Sec.  1.824 (Sec.  1.821(e)(2)(i)); and (2) a statement 
that the sequence information contained in the CRF, submitted under 
Sec.  1.821(e)(2)(i), is identical to the sequence information 
contained in the ``Sequence Listing'' submitted as a PDF image file 
(1.821(c)(2)) or on physical sheets of paper (1.821(c)(3)).
    Section 1.821(e)(3) is proposed to be added to set forth the 
requirements where a ``Sequence Listing'' in ASCII plain text format, 
in compliance with Sec.  1.824, has not been submitted for an 
international application under the Patent Cooperation Treaty (PCT); 
this application contains disclosures of nucleotide and/or amino acid 
sequences, as defined in paragraph (a) of this section and is to be 
searched by the United States International Searching Authority or 
examined by the United States International Preliminary Examining 
Authority. In such situations, the following are required: (1) A copy 
of the ``Sequence Listing'' in CRF, in accordance with the requirements 
of Sec.  1.824 (Sec.  1.821(e)(3)(i)); (2) a late furnishing fee for 
providing a ``Sequence Listing'' in response to an invitation, as set 
forth in Sec.  1.445(a)(5) (Sec.  1.821(e)(3)(ii)); and (3) a statement 
that the sequence information contained in the CRF submitted under 
Sec.  1.821(e)(3)(i) does not go beyond the disclosure in the 
international application as filed, or a statement that the information 
recorded in the ASCII plain text file submitted under Sec.  
1.821(e)(3)(i) is identical to the sequence listing contained in the 
international application as filed, as applicable (Sec.  
1.821(e)(3)(iii)).
    Section 1.821(e)(4) is proposed to be added to state that the CRF 
may not be retained as a part of the patent application file.
    Section 1.821(f) is proposed to be reserved. The text previously 
found in this section is now in Sec.  1.821(e)(2)(iii).
    Section 1.821(g) is proposed to be revised to delete reference to 
Sec.  1.821(f). Additionally, Sec.  1.821(g) is proposed to be revised 
to state that any amendment to add or replace a ``Sequence Listing'' 
and CRF copy thereof must be submitted in accordance with the 
requirements of Sec.  1.825.
    Section 1.821(h) is proposed to be revised to reference paragraphs 
(e)(3) of this section instead of paragraphs (b) through (f). Section 
1.821(h) is also proposed to be revised to add that a late furnishing 
fee, as set forth in Sec.  1.445(a)(5), is required where a ``Sequence 
Listing'' under PCT Rule 13ter is provided.
    Section 1.822: Section 1.822(b) is proposed to be revised to remove 
all prior references to WIPO Standard ST.25 (1998) and instead cross-
reference new Appendices A through F to part 1 of 37 CFR, subpart G, 
which would contain the updated 2009 version of the standard. 
Therefore, the statement regarding permission for incorporation by 
reference and information about the availability of ST.25 from WIPO's 
website is deleted.
    Section 1.822(c)(1) is proposed to be revised to remove the prior 
reference to WIPO Standard ST.25 (1998) and instead cross-reference new 
Appendix A to part 1 of 37 CFR, subpart G, which would contain the 
updated 2009 version of the standard.
    Section 1.822(c)(3) is proposed to be rewritten to replace 
instances of ``typed'' with ``listed.''
    Section 1.822(c)(5) is proposed to be rewritten to replace 
``presented'' with ``represented.''
    Section 1.822(c)(6) is proposed to be rewritten to delete ``be 
marked'' and instead state ``appear.''

[[Page 28308]]

    Section 1.822(d)(1) is proposed to be revised to remove the prior 
reference to WIPO Standard ST.25 (1998) and instead cross-reference new 
Appendix C to part 1 of 37 CFR, subpart G, which would contain the 
updated 2009 version of the standard. When providing reference to the 
sequence in the text of the description or claims, the numeric sequence 
identifier is preceded by SEQ ID NO: Or the like, even if the actual 
sequence is also embedded in the text of the description or claims of 
the patent application. The use of SEQ ID NO: Is preferred but 
including ``or the like'' is intended to ensure that a formalities 
notice is not sent when an application uses, for example, ``SEQ NO.'' 
or ``Seq. Id. No.'' or any similar identification for an amino acid or 
nucleotide sequence in the specification or claims where it is clear 
that a sequence from the ``Sequence Listing'' is shown in the 
description or claims.
    Section 1.822(d)(3) is proposed to be rewritten to replace 
``presented'' with ``represented.''
    Section 1.822(d)(4) is proposed to be rewritten to replace 
``presented'' with ``represented.''
    Section 1.822(d)(5) is proposed to be rewritten to replace the 
second occurrence of ``presented'' with ``represented.''
    Section 1.822(e) is proposed to be rewritten to replace ``that is 
made up'' with the term ``composed.''
    Section 1.823: The title of Sec.  1.823 is proposed to be rewritten 
as ``Requirements for content of a `Sequence Listing' part of the 
specification.''
    Section 1.823(a) is proposed to be rewritten to enumerate in Sec.  
1.823(a)(1) through (8) the content requirements for a ``Sequence 
Listing'' previously contained in Sec. Sec.  1.821(c), 1.823(a)(1), 
1.823(a)(2), and 1.823(b). Such requirements include, but are not 
limited to, sequence identifiers, the order and presentation of items 
of information, mandatory and optional information, the format as to 
line spacing, and the use of numeric identifiers.
    Section 1.823(b)(1) is proposed to include a requirement for 
applications other than an international application in the 
international stage to contain an express incorporation by reference of 
the material submitted as an ASCII plain text file via the USPTO patent 
electronic filing system or on read-only optical disc(s) into the 
specification of the patent application to identify the name of the 
file, the date of creation, and the size of the file in bytes.
    Section 1.823(b)(2) is proposed to specifically exempt the 
incorporation by reference requirement in Sec.  1.823(b)(1) from 
international applications during the international stage.
    Section 1.823(b)(3) is proposed to be added to specifically set 
forth the format and content for a ``Sequence Listing'' that is 
submitted either as a PDF image file via the USPTO patent electronic 
filing system or on physical sheets of paper, as enumerated in Sec.  
1.823(b)(3)(i) through (vi).
    Section 1.824: The title of Sec.  1.824 is proposed to be rewritten 
as ``Form and format for a nucleotide and/or amino acid sequence 
submission as an ASCII plain text file.''
    Section 1.824(a) is proposed to be reorganized for clarity and to 
apply to any ``Sequence Listing'' submission as an ASCII plain text 
file, rather than only to the CRF of a ``Sequence Listing.'' Section 
1.824(a)(1) is proposed to set forth the computer compatibilities and 
operating systems permitted. Section 1.824(a)(2) is proposed to 
indicate that ASCII plain text is required to be used, that all 
printable characters are permitted, and that no nonprintable characters 
are permitted, except ASCII Carriage Return plus ASCII Line Feed (CRLF) 
or Line Feed (LF) as line terminators. Section 1.824(a)(3) is proposed 
to set forth the naming convention for the ASCII plain text file of the 
``Sequence Listing.'' Section 1.824(a)(4) is proposed to indicate that 
no more than 74 printable characters can be present on any given line. 
This number represents a change from current rules (where 72 characters 
are permitted). This change is intended to conform to the number of 
characters of a sequence listing as printed in a granted patent or a 
pre-grant publication.
    Section 1.824(a)(5) is proposed to indicate that pagination is not 
permitted and that the ASCII plain text file must be one continuous 
file with no hard page breaks and no page numbering.
    Section 1.824(b) is proposed to indicate that the ASCII plain text 
file must contain a copy of a single ``Sequence Listing'' in a single 
file and may be submitted through either the USPTO patent electronic 
filing system or on read-only optical disc(s), in compliance with Sec.  
1.52(e). Section 1.824(b)(2) is proposed to provide that file 
compression may be used and to define the parameters for file 
compression for submission on a read-only optical disc. Section 1.824 
is proposed to be further revised to eliminate obsolete media on which 
the CRF of a ``Sequence Listing'' may be submitted. Section 1.824(c) is 
proposed to be eliminated, since the types of media available are 
specifically enumerated in Sec.  1.52(e). Section 1.824(d) is proposed 
to be eliminated, since the same provision is now included in Sec.  
1.52(e)(6).
    Section 1.825: Sections 1.825(a) and (b) are proposed to be 
rewritten to distinguish between a newly added ``Sequence Listing'' and 
an amended/replacement ``Sequence Listing'' submission, respectively. 
Sections 1.825(a) and (b) are proposed to be rewritten to state when a 
new or amended/replacement copy of the CRF is also required upon 
submission of a ``Sequence Listing.''
    Section 1.825(a) is proposed to be amended to provide for 
submission of a ``Sequence Listing'' not present on the application 
filing date (1) as an ASCII plain text file via either the USPTO patent 
electronic filing system or on a read-only optical disc, (2) as a PDF 
image file via the USPTO patent electronic filing system, or (3) on 
physical sheets of paper. The amendment adding the ``Sequence Listing'' 
must include a request that the amendment be made in one of two ways. 
First, a ``Sequence Listing'' submitted as an ASCII plain text file (in 
accordance with Sec.  1.825(a)(2)(i)) must be incorporated by reference 
in a separate paragraph of the specification. Second, a ``Sequence 
Listing'' submitted as a PDF image file via the USPTO patent electronic 
filing system (in accordance with Sec.  1.825(a)(2)(ii)) or on physical 
sheets of paper (in accordance with Sec.  1.825(a)(2)(iii)) must be 
placed after the abstract of the disclosure. Additionally, the 
``Sequence Listing'' must be submitted together with two statements. 
The first statement must indicate the basis for the amendment, with 
specific references to particular parts of the application as 
originally filed (specification, claims, drawings) for all sequence 
data in the ``Sequence Listing'' (Sec.  1.821(a)(3)). The second 
statement must indicate that the ``Sequence Listing'' contains no new 
matter (Sec.  1.821(a)(4)). Finally, if needed, Sec.  1.825(a)(5) 
provides that a new or substitute CRF must be submitted together with a 
statement, pursuant to Sec.  1.825(a)(6), that the sequence information 
contained in the CRF is the same as the sequence information contained 
in the ``Sequence Listing'' that had been submitted as a PDF image file 
via the USPTO patent electronic filing system or on physical sheets of 
paper.
    Section 1.825(b) is proposed to be updated to require an amended/
replacement ``Sequence Listing'' submitted: (1) As an ASCII plain text 
file via either the USPTO patent electronic filing system or on a read-

[[Page 28309]]

only optical disc (Sec.  1.825(b)(1)(i)), (2) as a PDF image file via 
the USPTO patent electronic filing system (Sec.  1.825(b)(1)(ii)), or 
(3) on physical sheets of paper (Sec.  1.825(b)(1)(iii)). The amended/
replacement ``Sequence Listing'' must include a request that it be made 
in one of two ways. First, a request that the amended/replacement 
``Sequence Listing,'' submitted as an ASCII plain text file, is 
incorporated by reference in a separate paragraph of the specification 
(replacing any prior such paragraph, as applicable) (Sec.  
1.825(b)(2)). The second way for such a request is by placing, after 
the abstract of the disclosure, the amended/replacement ``Sequence 
Listing'' that was submitted as a PDF image file via the USPTO patent 
electronic filing system or on physical sheets of paper (replacing any 
prior ``Sequence Listing,'' as applicable).
    The amended/replacement ``Sequence Listing'' must be submitted 
together with three statements. The first statement must identify the 
location of all deletions, replacements, or additions to the ``Sequence 
Listing'' (Sec.  1.825(b)(3)). The second statement must indicate the 
basis for the amendment, with specific references to particular parts 
of the application as originally filed (specification, claims, 
drawings) for all amended sequence data in the replacement ``Sequence 
Listing'' (Sec.  1.825(b)(4)). The third statement must indicate that 
the replacement ``Sequence Listing'' contains no new matter (Sec.  
1.825(b)(5)). Finally, if needed, a new or substitute CRF with the 
amendment incorporated therein (Sec.  1.825(b)(6)) must be submitted 
together with a statement that the sequence information contained in 
the CRF is the same as the sequence information contained in the 
replacement ``Sequence Listing'' submitted as a PDF image file via the 
USPTO patent electronic filing system or on physical sheets of paper 
(Sec.  1.825(b)(7)).
    Section 1.825(c) is proposed to replace current Sec.  1.825(c), 
which is proposed to be moved to Sec.  1.825(d). Section 1.825(c) 
relates to the required incorporation by reference statement when 
submitting a ``Sequence Listing'' under Sec.  1.821(c)(1). Should the 
application as originally filed not contain the incorporation by 
reference, then the application must be amended to contain such an 
incorporation by reference.
    Section 1.825(d) is proposed to contain the material from current 
Sec.  1.825(c).
    Subpart G of part 1: Appendices A through F are proposed to be 
added, explicitly incorporating the text of Tables 1-6, Appendix 2, 
WIPO Standard ST.25 (2009) into the CFR. Appendix G is proposed to be 
added to incorporate the table that was previously located in Sec.  
1.823.

Rulemaking Considerations

    A. Administrative Procedure Act: The changes proposed in this 
rulemaking involve rules of agency practice and procedure, and/or 
interpretive rules. See Bachow Commc'ns Inc. v. FCC, 237 F.3d 683, 690 
(D.C. Cir. 2001) (rules governing an application process are procedural 
under the Administrative Procedure Act); Inova Alexandria Hosp. v. 
Shalala, 244 F.3d 342, 350 (4th Cir. 2001) (rules for handling appeals 
are procedural where they do not change the substantive standard for 
reviewing claims); Nat'l Org. of Veterans' Advocates v. Sec'y of 
Veterans Affairs, 260 F.3d 1365, 1375 (Fed. Cir. 2001) (rule that 
clarifies interpretation of a statute is interpretive).
    Accordingly, prior notice and opportunity for public comment for 
the changes proposed in this rulemaking are not required pursuant to 5 
U.S.C. 553(b) or (c), or any other law. See Cooper Techs. Co. v. Dudas, 
536 F.3d 1330, 1336-37 (Fed. Cir. 2008) (stating that 5 U.S.C. 553, and 
thus 35 U.S.C. 2(b)(2)(B), do not require notice and comment rulemaking 
for ``interpretative rules, general statements of policy, or rules of 
agency organization, procedure, or practice'' (quoting 5 U.S.C. 
553(b)(A))). However, the USPTO has chosen to seek public comment 
before implementing the rule to benefit from the public's input.
    B. Regulatory Flexibility Act: Under the Regulatory Flexibility Act 
(5 U.S.C. 601 et seq.), whenever an agency is required by 5 U.S.C. 553 
(or any other law) to publish a notice of proposed rulemaking (NPRM), 
the agency must prepare and make available for public comment an 
Initial Regulatory Flexibility Analysis, unless the agency certifies 
under 5 U.S.C. 605(b) that the proposed rule, if implemented, will not 
have a significant economic impact on a substantial number of small 
entities. 5 U.S.C. 603, 605.
    For the reasons set forth herein, the Senior Counsel for Regulatory 
and Legislative Affairs of the USPTO has certified to the Chief Counsel 
for Advocacy of the Small Business Administration that this rule will 
not have a significant economic impact on a substantial number of small 
entities. See 5 U.S.C. 605(b).
    The USPTO proposes to amend the rules of practice to permit higher-
capacity physical media to be submitted to accommodate patent 
applications for certain inventions that require significant data in 
ASCII text format that exceed the capacity of the Office's electronic 
filing system. Additionally, extraction of compressed data files, which 
had not been permitted in the past for certain submissions, would be 
permitted if compliant with certain proposed new procedures. Other 
rules relating to certain obsolete and non-secure methods of presenting 
data would be eliminated. Lastly, this NPRM would remove an applicant's 
ability to rely on a previously submitted CRF of required sequence 
information (i.e., CRF transfer requests are eliminated). In light of 
the availability to download a ``Sequence Listing'' from granted U.S. 
patents and U.S. patent application publications via Public PAIR in the 
Supplemental Content tab, there is no longer a need for a CRF transfer.
    This rulemaking would make more flexible the process for submitting 
large amounts of data and streamline other procedural steps related to 
data files associated with patent applications. This rulemaking's 
proposed changes are largely procedural in nature, and do not impose 
any additional requirements or fees on applicants. For the foregoing 
reasons, the changes proposed in this NPRM will not have a significant 
economic impact on a substantial number of small entities.
    C. Executive Order 12866 (Regulatory Planning and Review): This 
rulemaking has been determined to be not significant for purposes of 
Executive Order 12866 (Sept. 30, 1993).
    D. Executive Order 13563 (Improving Regulation and Regulatory 
Review): The USPTO has complied with Executive Order 13563 (Jan. 18, 
2011). Specifically, to the extent feasible and applicable, the USPTO 
has: (1) Reasonably determined that the benefits of the rule justify 
its costs; (2) tailored the rule to impose the least burden on society 
consistent with obtaining the agency's regulatory objectives; (3) 
selected a regulatory approach that maximizes net benefits; (4) 
specified performance objectives; (5) identified and assessed available 
alternatives; (6) involved the public in an open exchange of 
information and perspectives among experts in relevant disciplines, 
affected stakeholders in the private sector, and the public as a whole, 
and provided online access to the rulemaking docket; (7) attempted to 
promote coordination, simplification, and harmonization across 
government agencies and identified goals designed to promote 
innovation; (8) considered approaches that reduce burdens while 
maintaining flexibility and freedom of choice for the public; and (9) 
ensured

[[Page 28310]]

the objectivity of scientific and technological information and 
processes.
    E. Executive Order 13132 (Federalism): This rulemaking does not 
contain policies with federalism implications sufficient to warrant 
preparation of a Federalism Assessment under Executive Order 13132 
(Aug. 4, 1999).
    F. Executive Order 13175 (Tribal Consultation): This rulemaking 
will not (1) have substantial direct effects on one or more Indian 
tribes; (2) impose substantial direct compliance costs on Indian tribal 
governments; or (3) preempt tribal law. Therefore, a tribal summary 
impact statement is not required under Executive Order 13175 (Nov. 6, 
2000).
    G. Executive Order 13211 (Energy Effects): This rulemaking is not a 
significant energy action under Executive Order 13211 because this 
rulemaking is not likely to have a significant adverse effect on the 
supply, distribution, or use of energy. Therefore, a Statement of 
Energy Effects is not required under Executive Order 13211 (May 18, 
2001).
    H. Executive Order 12988 (Civil Justice Reform): This rulemaking 
meets applicable standards to minimize litigation, eliminate ambiguity, 
and reduce burden as set forth in sections 3(a) and 3(b)(2) of 
Executive Order 12988 (Feb. 5, 1996).
    I. Executive Order 13045 (Protection of Children): This rulemaking 
does not concern an environmental risk to health or safety that may 
disproportionately affect children under Executive Order 13045 (Apr. 
21, 1997).
    J. Executive Order 12630 (Taking of Private Property): This 
rulemaking will not effect a taking of private property or otherwise 
have taking implications under Executive Order 12630 (Mar. 15, 1988).
    K. Congressional Review Act: Under the Congressional Review Act 
provisions of the Small Business Regulatory Enforcement Fairness Act of 
1996 (5 U.S.C. 801 et seq.), prior to issuing any final rule, the USPTO 
will submit a report containing the final rule and other required 
information to the United States Senate, the United States House of 
Representatives, and the Comptroller General of the Government 
Accountability Office. The changes in this rulemaking are not expected 
to result in an annual effect on the economy of $100 million or more, a 
major increase in costs or prices, or significant adverse effects on 
competition, employment, investment, productivity, innovation, or the 
ability of United States-based enterprises to compete with foreign-
based enterprises in domestic and export markets. Therefore, this 
rulemaking is not expected to result in a ``major rule'' as defined in 
5 U.S.C. 804(2).
    L. Unfunded Mandates Reform Act of 1995: The changes set forth in 
this rulemaking do not involve a Federal intergovernmental mandate that 
will result in the expenditure by State, local, and tribal governments, 
in the aggregate, of $100 million (as adjusted) or more in any one 
year, or a Federal private sector mandate that will result in the 
expenditure by the private sector of $100 million (as adjusted) or more 
in any one year, and will not significantly or uniquely affect small 
governments. Therefore, no actions are necessary under the provisions 
of the Unfunded Mandates Reform Act of 1995. See 2 U.S.C. 1501 et seq.
    M. National Environmental Policy Act of 1969: This rulemaking will 
not have any effect on the quality of the environment and is thus 
categorically excluded from review under the National Environmental 
Policy Act of 1969. See 42 U.S.C. 4321 et seq.
    N. National Technology Transfer and Advancement Act of 1995: The 
requirements of section 12(d) of the National Technology Transfer and 
Advancement Act of 1995 (15 U.S.C. 272 note) are not applicable because 
this rulemaking does not contain provisions that involve the use of 
technical standards.
    O. Paperwork Reduction Act of 1995: The Paperwork Reduction Act of 
1995 (44 U.S.C. 3501-3549) requires that the USPTO consider the impact 
of paperwork and other information collection burdens imposed on the 
public. In accordance with section 3507(d) of the Paperwork Reduction 
Act of 1995, the majority of the paperwork and other information 
collection burdens discussed in this proposed rule have already been 
approved under the following Office of Management and Budget (OMB) 
Control Numbers: 0651-0024 (Sequence Listing), 0651-0031 (Patent 
Processing), 0651-0032 (Initial Patent Applications), and 0651-0064 
(Patent Reexaminations and Supplemental Examinations).
    Modifications to 0651-0024 because of this proposed rulemaking will 
be submitted to OMB for approval prior to this rule becoming effective. 
Modifications include the removal of the Request for Transfer of a 
Computer Readable Form Under 37 CFR 1.821(e) (PTO/SB/93), which will 
result in a slight reduction in burden associated with this information 
collection. The USPTO estimates that this information collection's 
annual burden will decrease by 1,550 responses and 155 burden hours. 
These burden estimates are based on the current OMB approved burdens 
(response volumes) associated with this information collection, which 
may be different from any forecasts mentioned in other parts of this 
proposed rule.
    The changes discussed in this proposed rule do not affect the 
information collection requirements or burdens associated with 0651-
0031, 0651-0032 and 0651-0064 listed above; therefore, the USPTO does 
not plan to take any additional actions on these information 
collections as a result of this rulemaking. Notwithstanding any other 
provision of law, no person is required to respond to, nor shall a 
person be subject to a penalty for failure to comply with, a collection 
of information subject to the requirements of the Paperwork Reduction 
Act unless that collection of information has a currently valid OMB 
control number.
    P. E-Government Act Compliance: The USPTO is committed to 
compliance with the E-Government Act to promote the use of the internet 
and other information technologies, to provide increased opportunities 
for citizen access to Government information and services, and for 
other purposes.

List of Subjects in 37 CFR Part 1

    Administrative practice and procedure, Biologics, Courts, Freedom 
of information, Inventions and patents, Reporting and recordkeeping 
requirements, Small businesses.

    For the reasons stated in the preamble and under the authority 
contained in 35 U.S.C. 2, as amended, the USPTO proposes to amend 37 
CFR part 1 as follows:

PART 1--RULES OF PRACTICE IN PATENT CASES

0
1. The authority citation for 37 CFR part 1 continues to read as 
follows:

    Authority:  35 U.S.C. 2(b)(2), unless otherwise noted.

0
2. Amend Sec.  1.52 by revising the heading and paragraphs (e) and (f) 
to read as follows:


Sec.  1.52  Language, paper, writing, margins, read-only optical disc 
specifications.

* * * * *
    (e) Electronic documents submitted on a read-only optical disc that 
are to become part of the permanent United States Patent and Trademark 
Office records in the file of a patent application, reexamination, or 
supplemental examination proceeding. (1) The following documents may be 
submitted to the Office on a read-only

[[Page 28311]]

optical disc in compliance with this paragraph:
    (i) A ``Computer Program Listing Appendix'' (see Sec.  1.96(c));
    (ii) A ``Sequence Listing'' (submitted under Sec.  1.821(c) in 
compliance with Sec.  1.824); or
    (iii) ``Large Tables'' (see Sec.  1.58(c)).
    (2) Read-only optical disc as used in this part means a finalized 
disc in conformance with International Organization for Standardization 
(ISO) 9660, on which the data is recorded so it is permanent and cannot 
be changed or erased, and is one of:
    (i) Compact Disc-Read-Only Memory (CD-ROM) or a Compact Disc-
Recordable (CD-R); or
    (ii) Digital Video Disc-Recordable (DVD-R or DVD+R);
    (3) Each read-only optical disc must conform to the following 
requirements:
    (i) Computer compatibility: PC or Mac[supreg];
    (ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], MacOS[supreg], or Unix[supreg]/Linux[supreg];
    (iii) The contents of each read-only optical disc must be in 
American Standard Code for Information Interchange (ASCII) plain text 
and if compressed, must be compressed in accordance with Sec. Sec.  
1.58, 1.96, and 1.824, as applicable.
    (4) Each read-only optical disc must be enclosed in a hard case 
within an unsealed, padded, and protective mailing envelope, and must 
be accompanied by a transmittal letter in accordance with paragraph (a) 
of this section, including the following information:
    (i) First-named inventor (if known);
    (ii) Title of the invention;
    (iii) Attorney docket or file reference number (if applicable);
    (iv) Application number and filing date (if known);
    (v) The operating system (MS-DOS[supreg], MS-Windows[supreg], Mac 
OS[supreg], or Unix[supreg]/Linux[supreg]) used to produce the disc; 
and
    (vi) The file(s) contained on the read-only optical disc, including 
the name of the file, the size of the file in bytes, and the date of 
creation.
    (5) Each read-only optical disc must have a label permanently 
affixed thereto on which the following information has been hand-
printed or typed:
    (i) First-named inventor (if known);
    (ii) Title of the invention;
    (iii) Attorney docket or file reference number (if applicable);
    (iv) Application number and filing date (if known);
    (v) Date on which the data were recorded on the read-only optical 
disc; and
    (vi) Disc order (e.g., ``1 of X''), if multiple read-only optical 
discs are submitted.
    (6) Read-only optical discs will not be returned to the applicant 
and may not be retained as part of the patent application file.
    (7) Any amendment to the information on a read-only optical disc 
must be by way of a replacement read-only optical disc, in compliance 
with Sec.  1.58(g) for ``Large Tables,'' Sec.  1.96(c)(5) for a 
``Computer Program Listing Appendix,'' and Sec.  1.825(b) for a 
``Sequence Listing'' or Computer Readable Form (CRF) of a ``Sequence 
Listing.''
    (8) The specification must contain an incorporation by reference of 
the material on each read-only optical disc in a separate paragraph 
(Sec.  1.77(b)(5)), identifying the name of each file, their date of 
creation, and their size in bytes, except for an international 
application in the international stage. The Office may require the 
applicant to amend the specification to include the material 
incorporated by reference.
    (9) If a file is unreadable, it will be treated as not having been 
submitted, and a notice will be issued to supply a compliant 
submission.
    (f) Determining application size fees for applications containing 
electronic documents submitted on a read-only optical disc or via the 
USPTO patent electronic filing system--(1) Submission on Read-Only 
Optical Discs: The application size fee required by Sec.  1.16(s) or 
1.492(j), for an application component submitted in part on a read-only 
optical disc in compliance with paragraph (e) of this section, shall be 
determined such that each three kilobytes of content submitted on a 
read-only optical disc shall be counted as a sheet of paper. Excluded 
from this determination is any ASCII plain text file submitted on a 
read-only optical disc under paragraph (e) of this section containing:
    (i) Any ``Sequence Listing'' or CRF of a ``Sequence Listing'' in 
compliance with Sec.  1.821(c) or (e); or
    (ii) Any ``Computer Program Listing Appendix'' in compliance with 
Sec.  1.96(c).
    (2) Submission via the USPTO Patent Electronic Filing System: The 
application size fee required by Sec.  1.16(s) or 1.492(j), for an 
application submitted in whole or in part via the USPTO patent 
electronic filing system, shall be determined such that the paper size 
equivalent will be considered to be 75% of the number of sheets of 
paper present in the specification and drawings of the application when 
entered into the Office file wrapper after being rendered by the USPTO 
patent electronic filing system. Excluded from this determination is 
any ASCII plain text file submitted via the USPTO patent electronic 
filing system containing:
    (i) Any ``Sequence Listing'' or CRF of a ``Sequence Listing,'' in 
compliance with Sec.  1.821(c) or (e); or
    (ii) Any ``Computer Program Listing Appendix'' in compliance with 
Sec.  1.96(c).
    (3) Any submission of a ``Sequence Listing'' in electronic form of 
300 MB-800 MB filed in an application under 35 U.S.C. 111 or 371 will 
be subject to the fee set forth in Sec.  1.21(o)(1). Any submission of 
a ``Sequence Listing'' filed in electronic form that exceeds 800 MB in 
an application under 35 U.S.C. 111 or 371 will be subject to the fee 
set forth in Sec.  1.21(o)(2).
0
3. Amend Sec.  1.58 by revising paragraphs (b) and (c) and adding 
paragraphs (d) through (j) to read as follows:


Sec.  1.58  Chemical and mathematical formulas and tables.

* * * * *
    (b) Chemical and mathematical formulas and tables must be presented 
in compliance with Sec.  1.52(a) and (b), except that chemical and 
mathematical formulas or tables may be placed in a landscape 
orientation if they cannot be presented satisfactorily in a portrait 
orientation. Typewritten characters used in such formulas and tables 
must be chosen from a block (nonscript) type font or lettering style 
having capital letters that should be at least 0.422 cm (0.166 inches) 
high (e.g., preferably Arial, Times Roman, or Courier, with a font size 
of 12 point), but may be no smaller than 0.21cm (0.08 inches) high 
(e.g., a font size of 6 point). A space at least 0.64 cm (0.25 inches) 
high should be provided between complex formulas and tables and the 
text. Chemical and mathematical formulas must be configured to maintain 
the proper positioning of their characters when displayed in order to 
preserve their intended meaning. Tables should have the lines and 
columns of data closely spaced to conserve space, consistent with a 
high degree of legibility.
    (c) The following ``Large Tables'' may be submitted in electronic 
form in ASCII plain text via the USPTO patent electronic filing system 
or on a read-only optical disc, in compliance with Sec.  1.52(e), 
excluding an international application during the international stage:
    (1) Any individual table that is more than 50 pages in length; or
    (2) Multiple tables, if the total number of pages of all the tables 
in an

[[Page 28312]]

application exceeds 100 pages in length, where a table page is a page 
printed on paper, in conformance with paragraph (b) of this section.
    (d) ``Large Tables'' submitted in electronic form in ASCII plain 
text must conform to the following requirements:
    (1) Must maintain the spatial relationships (e.g., alignment of 
columns and rows) of the table elements when displayed to visually 
preserve the relational information they convey.
    (2) Must have the following compatibilities:
    (i) Computer compatibility: PC or Mac[supreg];
    (ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg].
    (3) Must be in ASCII plain text, where:
    (i) All printable characters (including the space character) are 
permitted;
    (ii) No nonprintable (ASCII control) characters are permitted, 
except ASCII Carriage Return plus ASCII Line Feed (CRLF) or Line Feed 
(LF) as line terminators.
    (4) Must be named as *.txt, where ``*'' is one character or a 
combination of characters limited to upper- or lowercase letters, 
numbers, hyphens, and underscores and does not exceed 60 characters in 
total, excluding the extension. No spaces or other types of characters 
are permitted in the file name.
    (5) Must be incorporated by reference in a separate paragraph of 
the specification, in accordance with Sec.  1.77(b)(5).
    (e) ``Large Tables'' submitted via the USPTO patent electronic 
filing system must not exceed 25 MB, and file compression is not 
permitted.
    (f) ``Large Tables'' submitted in compliance with Sec.  1.52(e) via 
read-only optical disc, must meet the following requirements:
    (1) The ASCII plain text file may be compressed using 
WinZip[supreg], 7-Zip, or Unix[supreg]/Linux[supreg] Zip;
    (2) A compressed file must not be self-extracting; and
    (3) A compressed ASCII plain text file that does not fit on a 
single read-only optical disc may be split into multiple file parts in 
accordance with the target read-only optical disc size and labeled in 
compliance with Sec.  1.52(e)(5)(vi).
    (g) Any amendments to ``Large Tables'' in electronic form in ASCII 
plain text format must include:
    (1) A replacement ASCII plain text file, in accordance with the 
requirements of paragraphs (d) through (f) of this section, submitted 
via the USPTO patent electronic filing system or on a read-only optical 
disc, in compliance with Sec.  1.52(e), labeled as ``REPLACEMENT MM/DD/
YYYY'' (with the month, day, and year of creation indicated);
    (2) A request that the amendment be made by incorporation by 
reference of the material in the replacement ASCII plain text file, in 
a separate paragraph of the specification (replacing any prior such 
paragraph, as applicable) identifying the name of the file, the date of 
creation, and the size of the file in bytes (see Sec.  1.77(b)(5));
    (3) A statement that identifies the location of all deletions, 
replacements, or additions to the ASCII plain text file; and
    (4) A statement that the replacement ASCII plain text file contains 
no new matter.
    (h) The specification of an application with ``Large Tables'' as an 
ASCII plain text file, present on the application filing date, without 
an incorporation by reference of the material contained in the ASCII 
plain text file, must be amended to contain a separate paragraph 
incorporating by reference the material contained in the ASCII plain 
text file, in accordance with Sec.  1.77(b)(5).
    (i) Any read-only optical disc for ``Large Tables'' must be 
submitted in duplicate. The read-only optical disc and duplicate copy 
must be labeled ``Copy 1'' and ``Copy 2,'' respectively. The 
transmittal letter that accompanies the read-only optical discs must 
include a statement that the two read-only optical discs are identical. 
In the event that the two read-only optical discs are not identical, 
the Office will use the read-only optical disc labeled ``Copy 1'' for 
further processing.
    (j) Any amendment to the information on a read-only optical disc 
must be by way of a replacement read-only optical disc, in compliance 
with Sec.  1.58(g), where the replacement read-only optical disc and 
copy must be labeled ``COPY 1 REPLACEMENT MM/DD/YYYY'' (with the month, 
day, and year of creation indicated), and ``COPY 2 REPLACEMENT MM/DD/
YYYY,'' respectively.
0
4. Amend Sec.  1.71 by revising paragraph (f) to read as follows:


Sec.  1.71  Detailed description and specification of the invention.

* * * * *
    (f) The specification must commence on a separate sheet. Each sheet 
including part of the specification may not include other parts of the 
application or other information. The claim(s), abstract, and 
``Sequence Listing'' (if required or submitted under Sec.  1.821(c)) 
should not be included on a sheet including any other part of the 
application.
* * * * *
0
5. Amend Sec.  1.77 by revising paragraphs (b)(5) and (13) to read as 
follows:


Sec.  1.77  Arrangement of application elements.

* * * * *
    (b) * * *
    (5) An incorporation by reference statement regarding the material 
on the one or more ASCII plain text files, submitted via the USPTO 
patent electronic filing system or on one or more read-only optical 
discs (see Sec.  1.52(e)(8)), identifying the names of each file, the 
date of creation of each file, and the size of each file in bytes, for 
the following document types:
    (i) A ``Computer Program Listing Appendix'' (see Sec.  1.96(c));
    (ii) A ``Sequence Listing'' (see Sec.  1.821(c)); or
    (iii) ``Large Tables'' (see Sec.  1.58(c)).
* * * * *
    (13) ``Sequence Listing,'' required by Sec.  1.821(c), that is 
submitted as a Portable Document Format (PDF) file (as set forth in 
Sec.  1.821(c)(1)(ii)) via the USPTO patent electronic filing system or 
on physical sheets of paper (as set forth in Sec.  1.821(c)(1)(iii)).
* * * * *
0
6. Amend Sec.  1.96 by revising paragraphs (a) and (c) to read as 
follows:


Sec.  1.96  Submission of computer program listings.

    (a) General. Descriptions of the operation and general content of 
computer program listings should appear in the description portion of 
the specification. A computer program listing for the purpose of this 
section is defined as a document that lists in appropriate sequence the 
instructions, routines, and other contents of a program for a computer. 
The program listing may be either in machine or machine-independent 
(object or source) language that will cause a computer to perform a 
desired procedure or task such as solve a problem, regulate the flow of 
work in a computer, or control or monitor events. Computer program 
listings may be submitted in patent applications, as set forth in 
paragraphs (b) and (c) of this section.
* * * * *
    (c) As an appendix that will not be printed: Any computer program 
listing may, and any computer program listing having over 300 lines (up 
to 72 characters per line) must, be submitted as an electronic document 
in ASCII plain text, whether submitted via the

[[Page 28313]]

USPTO patent electronic filing system or on a read-only optical disc, 
in compliance with Sec.  1.52(e). An electronic document containing 
such a computer program listing is to be referred to as a ``Computer 
Program Listing Appendix.'' The ``Computer Program Listing Appendix'' 
will not be part of the printed patent. The specification must include 
an incorporation by reference of the ``Computer Program Listing 
Appendix,'' in accordance with Sec.  1.77(b)(5).
    (1) A ``Computer Program Listing Appendix'' must conform to the 
following requirements:
    (i) Computer compatibility: PC or Mac[supreg];
    (ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg];
    (iii) Line terminator: ASCII CRLF or LF only; and
    (iv) Control Codes: The data must not be dependent on control 
characters or codes that are not defined in the ASCII character set.
    (2) Each file must be named as *.txt, where ``*'' is one character 
or a combination of characters limited to upper- or lowercase letters, 
numbers, hyphens, and underscores and does not exceed 60 characters in 
total, excluding the extension. No spaces or other types of characters 
are permitted in the file name.
    (3) Each file containing a ``Computer Program Listing Appendix'' 
submitted via the USPTO patent electronic filing system must not exceed 
25 MB, and file compression is not permitted.
    (4) A ``Computer Program Listing Appendix'' submitted in compliance 
with Sec.  1.52(e) must conform to the following requirements:
    (i) A separate read-only optical disc containing a ``Computer 
Program Listing Appendix'' must be submitted for each applicable 
application;
    (ii) Multiple computer program listings for a single application 
may be placed on a single read-only optical disc;
    (iii) Multiple read-only optical discs, containing one or more 
computer program listings, may be submitted for a single application, 
if necessary;
    (iv) Any computer program listing may, and a computer program 
listing having a nested file structure must, when submitted in 
compliance with Sec.  1.52(e), be compressed into a single file using 
WinZip[supreg], 7-Zip, or Unix[supreg]/Linux[supreg] Zip;
    (v) Any compressed file must not be self-extracting; and
    (vi) A compressed ASCII plain text file that does not fit on a 
single read-only optical disc may be split into multiple file parts, in 
accordance with the target read-only optical disc size and labeled in 
compliance with Sec.  1.52(e)(5)(vi).
    (5) Any amendments to a ``Computer Program Listing Appendix'' in 
electronic form in ASCII plain text format must include:
    (i) A replacement ASCII plain text file, in accordance with the 
requirements of paragraph (c) of this section, via the USPTO patent 
electronic filing system, or on a read-only optical disc, in compliance 
with Sec.  1.52(e) and labeled as ``COPY 1 REPLACEMENT MM/DD/YYYY'' 
(with the month, day, and year of creation indicated) and ``COPY 2 
REPLACEMENT MM/DD/YYYY;''
    (ii) A request that the amendment be made by incorporation by 
reference of the material in the replacement ASCII plain text file, in 
a separate paragraph of the specification (replacing any prior such 
paragraph) identifying the name of the file, the date of creation, and 
the size of the file in bytes (see Sec.  1.77(b)(5));
    (iii) A statement that identifies the location of all deletions, 
replacements, or additions to the ASCII plain text file; and
    (iv) A statement that the replacement ASCII plain text file 
contains no new matter.
    (6) The specification of a complete application with a ``Computer 
Program Listing Appendix'' as an ASCII plain text file, filed on the 
application filing date, without an incorporation by reference of the 
material contained in the ASCII plain text file, must be amended to 
contain a separate paragraph incorporating by reference the material 
contained in the ASCII plain text file, in accordance with Sec.  
1.77(b)(5).
    (7) Any read-only optical disc for a ``Computer Program Listing 
Appendix'' must be submitted in duplicate. The read-only optical disc 
and duplicate copy must be labeled ``Copy 1'' and ``Copy 2,'' 
respectively. The transmittal letter that accompanies the read-only 
optical discs must include a statement that the two read-only optical 
discs are identical. In the event that the two read-only optical discs 
are not identical, the Office will use the read-only optical disc 
labeled ``Copy 1'' for further processing. Any amendment to the 
information on a read-only optical disc must be by way of a replacement 
read-only optical disc, in compliance with Sec.  1.96(c)(5).
0
7. Amend Sec.  1.121 by revising paragraph (b) introductory text and 
adding paragraph (b)(6) to read as follows:


Sec.  1.121  Manner of making amendments in applications.

* * * * *
    (b) Specification. Amendments to the specification, other than the 
claims, ``Large Tables (Sec.  1.58(c)), a ``Computer Program Listing 
Appendix'' (Sec.  1.96(c)(5) and (7)), and a ``Sequence Listing'' or 
CRF (Sec.  1.825), must be made by adding, deleting, or replacing a 
paragraph; by replacing a section; or by a substitute specification, in 
the manner specified in this section.
* * * * *
    (6) Changes to ``Large Tables,'' a ``Computer Program Listing 
Appendix,'' or a ``Sequence Listing'' must be made in accordance with 
Sec.  1.58(g) for ``Large Tables,'' Sec.  1.96(c)(5) for a ``Computer 
Program Listing Appendix,'' and Sec.  1.825 for a ``Sequence Listing.''
* * * * *
0
8. Amend Sec.  1.173 by revising paragraphs (b)(1) and (d) to read as 
follows:


Sec.  1.173  Reissue specification, drawings, and amendments.

* * * * *
    (b) * * *
    (1) Specification other than the claims, ``Large Tables'' (Sec.  
1.58(c)), a ``Computer Program Listing Appendix'' (Sec.  1.96(c)), or a 
``Sequence Listing'' (Sec.  1.821(c)). (i) Changes to the 
specification, other than to the claims, ``Large Tables'' (Sec.  
1.58(c)), a ``Computer Program Listing Appendix'' (Sec.  1.96(c)), or a 
``Sequence Listing'' (Sec.  1.821(c)), must be made by submission of 
the entire text of an added or rewritten paragraph, including markings 
pursuant to paragraph (d) of this section, except that an entire 
paragraph may be deleted by a statement deleting the paragraph, without 
presentation of the text of the paragraph. The precise point in the 
specification where any added or rewritten paragraph is located must be 
identified.
    (ii) Changes to ``Large Tables,'' a ``Computer Program Listing 
Appendix,'' or a ``Sequence Listing'' must be made in accordance with 
Sec.  1.58(g) for ``Large Tables,'' Sec.  1.96(c)(5) for a ``Computer 
Program Listing Appendix,'' and Sec.  1.825 for a ``Sequence Listing.''
* * * * *
    (d) Changes shown by markings. Any changes relative to the patent 
being reissued that are made to the specification, including the claims 
but excluding ``Large Tables,'' a ``Computer Program Listing 
Appendix,'' or a ``Sequence Listing,'' upon filing or by an amendment 
paper in the reissue application, must include the following markings:

[[Page 28314]]

    (1) The matter to be omitted by reissue must be enclosed in 
brackets; and
    (2) The matter to be added by reissue must be underlined.
* * * * *
0
9. Amend Sec.  1.530 by revising paragraph (d)(1) to read as follows:


Sec.  1.530  Statement by patent owner in ex parte reexamination; 
amendment by patent owner in ex parte or inter partes reexamination; 
inventorship change in ex parte or inter partes reexamination.

* * * * *
    (d) * * *
    (1) Specification other than the claims, ``Large Tables'' (Sec.  
1.58(c)), a ``Computer Program Listing Appendix'' (Sec.  1.96(c)), or a 
``Sequence Listing'' (Sec.  1.821(c)).
    (i) Changes to the specification, other than to the claims, ``Large 
Tables'' (Sec.  1.58(c)), a ``Computer Program Listing Appendix'' 
(Sec.  1.96(c)), or a ``Sequence Listing'' (Sec.  1.821(c)), must be 
made by submission of the entire text of an added or rewritten 
paragraph, including markings pursuant to paragraph (f) of this 
section, except that an entire paragraph may be deleted by a statement 
deleting the paragraph, without presentation of the text of the 
paragraph. The precise point in the specification where any added or 
rewritten paragraph is located must be identified.
    (ii) Changes to ``Large Tables,'' a ``Computer Program Listing 
Appendix,'' or a ``Sequence Listing'' must be made, in accordance with 
Sec.  1.58(g) for ``Large Tables,'' Sec.  1.96(c)(5) for a ``Computer 
Program Listing Appendix,'' and Sec.  1.825 for a ``Sequence Listing.''
* * * * *
0
10. Amend Sec.  1.821 by revising paragraphs (a), and (c) through (e), 
removing and reserving paragraph (f), and revising paragraphs (g) 
through (h) to read as follows:


Sec.  1.821  Nucleotide and/or amino acid sequence disclosures in 
patent applications.

    (a) Nucleotide and/or amino acid sequences, as used in Sec. Sec.  
1.821 through 1.825, are interpreted to mean an unbranched sequence of 
4 or more amino acids or an unbranched sequence of 10 or more 
nucleotides. Branched sequences are specifically excluded from this 
definition. Sequences with fewer than four specifically defined 
nucleotides or amino acids are specifically excluded from this section. 
``Specifically defined'' means those amino acids other than ``Xaa'' and 
those nucleotide bases other than ``n,'' defined in accordance with 
Appendices A through F to this subpart. Nucleotides and amino acids are 
further defined as follows:
    (1) Nucleotides: Nucleotides are intended to embrace only those 
nucleotides that can be represented using the symbols set forth in 
Appendix A to this subpart. Modifications (e.g., methylated bases) may 
be described as set forth in Appendix B to this subpart, but shall not 
be shown explicitly in the nucleotide sequence.
    (2) Amino acids: Amino acids are those L-amino acids commonly found 
in naturally occurring proteins and are listed in Appendix C to this 
subpart. Those amino acid sequences containing D-amino acids are not 
intended to be embraced by this definition. Any amino acid sequence 
that contains post-translationally modified amino acids may be 
described as the amino acid sequence that is initially translated using 
the symbols shown in Appendix C to this subpart with the modified 
positions (e.g., hydroxylations or glycosylations) being described as 
set forth in Appendix D to this subpart, but these modifications shall 
not be shown explicitly in the amino acid sequence. Any peptide or 
protein that can be expressed as a sequence using the symbols in 
Appendix C to this subpart, in conjunction with a description in the 
Feature section, to describe, for example, modified linkages, cross 
links and end caps, non-peptidyl bonds, etc., is embraced by this 
definition.

    Note 1 to paragraph (a):  Appendices A through F contain Tables 
1-6 of the World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009).

* * * * *
    (c) Patent applications that contain disclosures of nucleotide and/
or amino acid sequences, as defined in paragraph (a) of this section, 
must contain a ``Sequence Listing'' as a separate part of the 
specification containing each of those nucleotide and/or amino acid 
sequences and associated information using the symbols and format in 
accordance with the requirements of Sec. Sec.  1.822 and 1.823. The 
``Sequence Listing'' must be submitted as follows, except for a 
national stage entry under Sec.  1.495(b)(1), where the ``Sequence 
Listing'' has been previously communicated by the International Bureau 
or originally filed in the United States Patent and Trademark Office 
and complies with Patent Cooperation Treaty (PCT) Rule 5.2:
    (1) As an ASCII plain text file, in compliance with Sec.  1.824, 
submitted via the USPTO patent electronic filing system or on a read-
only optical disc under Sec.  1.52(e), accompanied by an incorporation 
by reference statement of the ASCII plain text file, in a separate 
paragraph of the specification, in accordance with Sec.  1.77(b)(5);
    (2) As a PDF file via the USPTO patent electronic filing system; or
    (3) On physical sheets of paper.
    (d) Where the description or claims of a patent application discuss 
a sequence that is set forth in the ``Sequence Listing,'' in accordance 
with paragraph (c) of this section, reference must be made to the 
sequence by use of a sequence identifier (Sec.  1.823(a)(5)), preceded 
by ``SEQ ID NO:'' In the text of the description or claims, even if the 
sequence is also embedded in the text of the description or claims of 
the patent application. Where a sequence is presented in a drawing, 
reference must be made to the sequence by use of the sequence 
identifier (Sec.  1.823(a)(5)), either in the drawing or in the Brief 
Description of the Drawings, where the correlation between multiple 
sequences in the drawing and their sequence identifiers (Sec.  
1.823(a)(5)) in the Brief Description is clear.
    (e)(1) If the ``Sequence Listing'' under paragraph (c) is submitted 
in an application filed under 35 U.S.C. 111(a) as a PDF file (Sec.  
1.821(c)(2)) via the USPTO patent electronic filing system or on 
physical sheets of paper (Sec.  1.821(c)(3)), then the following must 
be submitted:
    (i) A CRF of the ``Sequence Listing,'' in accordance with the 
requirements of Sec.  1.824; and
    (ii) A statement that the sequence information contained in the CRF 
submitted under paragraph (e)(1)(i) of this section is identical to the 
sequence information contained in the ``Sequence Listing'' under 
paragraph (c) of this section.
    (2) If the ``Sequence Listing'' under paragraph (c) of this section 
in an application submitted under 35 U.S.C. 371 is a PDF file (Sec.  
1.821(c)(2)) or on physical sheets of paper (Sec.  1.821(c)(3)), and 
not also as an ASCII plain text file, in compliance with Sec.  1.824 
(Sec.  1.821(c)(1)), then the following must be submitted:
    (i) A CRF of the ``Sequence Listing,'' in accordance with the 
requirements of Sec.  1.824; and
    (ii) A statement that the sequence information contained in the CRF 
submitted under paragraph (e)(2)(i) of this section is identical to the 
sequence information contained in the ``Sequence Listing'' under 
paragraph (c)(2) or (3) of this section.

[[Page 28315]]

    (3) If a ``Sequence Listing'' in ASCII plain text format, in 
compliance with Sec.  1.824, has not been submitted for an 
international application under the PCT, and that application contains 
disclosures of nucleotide and/or amino acid sequences, as defined in 
paragraph (a) of this section, and is to be searched by the United 
States International Searching Authority or examined by the United 
States International Preliminary Examining Authority, then the 
following must be submitted:
    (i) A CRF of the ``Sequence Listing,'' in accordance with the 
requirements of Sec.  1.824;
    (ii) The late furnishing fee for providing a ``Sequence Listing'' 
in response to an invitation, as set forth in Sec.  1.445(a)(5); and
    (iii) A statement that the sequence information contained in the 
CRF, submitted under paragraph (e)(3)(i) of this section, does not go 
beyond the disclosure in the international application as filed, or a 
statement that the information recorded in the ASCII plain text file, 
submitted under paragraph (e)(3)(i) of this section, is identical to 
the sequence listing contained in the international application as 
filed, as applicable.
    (4) The CRF may not be retained as a part of the patent application 
file.
    (f) [Reserved]
    (g) If any of the requirements of paragraphs (b) through (e) of 
this section are not satisfied at the time of filing under 35 U.S.C. 
111(a) or at the time of entering the national stage under 35 U.S.C. 
371, the applicant will be notified and given a period of time within 
which to comply with such requirements in order to prevent abandonment 
of the application. Any amendment to add or replace a ``Sequence 
Listing'' and CRF copy thereof in reply to a requirement under this 
paragraph must be submitted in accordance with the requirements of 
Sec.  1.825.
    (h) If any of the requirements of paragraph (e)(3) of this section 
are not satisfied at the time of filing an international application 
under the PCT, and the application is to be searched by the United 
States International Searching Authority or examined by the United 
States International Preliminary Examining Authority, the applicant may 
be sent a notice necessitating compliance with the requirements within 
a prescribed time period. Where a ``Sequence Listing'' under PCT Rule 
13ter is provided in reply to a requirement under this paragraph, it 
must be accompanied by a statement that the information recorded in the 
ASCII plain text file under paragraph (e)(3)(i) of this section is 
identical to the sequence listing contained in the international 
application as filed, or does not go beyond the disclosure in the 
international application as filed, as applicable. It must also be 
accompanied by the late furnishing fee, as set forth in Sec.  
1.445(a)(5). If the applicant fails to timely provide the required CRF, 
the United States International Searching Authority shall search only 
to the extent that a meaningful search can be performed without the 
CRF, and the United States International Preliminary Examining 
Authority shall examine only to the extent that a meaningful 
examination can be performed without the CRF.
0
11. Amend Sec.  1.822 by revising paragraphs (b), (c)(1), (3), (5) and 
(6), (d)(1), (3) through (5), and (e) to read as follows:


Sec.  1.822  Symbols and format to be used for nucleotide and/or amino 
acid sequence data.

* * * * *
    (b) The code for representing the nucleotide and/or amino acid 
sequence characters shall conform to the code set forth in Appendices A 
and C to this subpart. No code other than that specified in these 
sections shall be used in nucleotide and amino acid sequences. A 
modified base or modified or unusual amino acid may be presented in a 
given sequence as the corresponding unmodified base or amino acid if 
the modified base or modified or unusual amino acid is one of those 
listed in Appendices B and D to this subpart, and the modification is 
also set forth in the Feature section. Otherwise, each occurrence of a 
base or amino acid not appearing in Appendices A and C, shall be listed 
in a given sequence as ``n'' or ``Xaa,'' respectively, with further 
information, as appropriate, given in the Feature section, by including 
one or more feature keys listed in Appendices E and F to this subpart.

    Note 1 to paragraph (b): Appendices A through F contain Tables 
1-6 of the World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009).

    (c) * * *
    (1) A nucleotide sequence shall be listed using the lowercase 
letter for representing the one-letter code for the nucleotide bases 
set forth in Appendix A to this subpart.
* * * * *
    (3) The bases in the coding parts of a nucleotide sequence shall be 
listed as triplets (codons). The amino acids corresponding to the 
codons in the coding parts of a nucleotide sequence shall be listed 
immediately below the corresponding codons. Where a codon spans an 
intron, the amino acid symbol shall be listed below the portion of the 
codon containing two nucleotides.
* * * * *
    (5) A nucleotide sequence shall be represented, only by a single 
strand, in the 5 to 3 direction, from left to right.
    (6) The enumeration of nucleotide bases shall start at the first 
base of the sequence with number 1. The enumeration shall be continuous 
through the whole sequence in the direction 5 to 3. The enumeration 
shall appear in the right margin, next to the line containing the one-
letter codes for the bases, and giving the number of the last base of 
that line.
* * * * *

    Note 2 to paragraph (c): Appendices A through F contain Tables 
1-6 of the World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009).

    (d) * * *
    (1) The amino acids in a protein or peptide sequence shall be 
listed using the three-letter abbreviation, with the first letter as an 
uppercase character, as in Appendix C to this subpart.
* * * * *
    (3) An amino acid sequence shall be represented in the amino to 
carboxy direction, from left to right, and the amino and carboxy groups 
shall not be represented in the sequence.
    (4) The enumeration of amino acids may start at the first amino 
acid of the first mature protein, with the number 1. When represented, 
the amino acids preceding the mature protein (e.g., pre-sequences, pro-
sequences, pre-pro-sequences and signal sequences) shall have negative 
numbers, counting backwards starting with the amino acid next to number 
1. Otherwise, the enumeration of amino acids shall start at the first 
amino acid at the amino terminal as number 1, and shall appear below 
every 5 amino acids of the sequence. The enumeration method for amino 
acid sequences that is set forth in this section remains applicable for 
amino acid sequences that are circular in configuration, with the 
exception that the designation of the first amino acid of the sequence 
may be made at the option of the applicant.
    (5) An amino acid sequence that contains internal terminator 
symbols (e.g., ``Ter,'' ``*,'' or ``.,'' etc.) may not be

[[Page 28316]]

represented as a single amino acid sequence but shall be represented as 
separate amino acid sequences.

    Note 3 to paragraph (d): Appendices A through F contain Tables 
1--6 of the World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009).

    (e) A sequence with a gap or gaps shall be represented as a 
plurality of separate sequences, with separate sequence identifiers 
(Sec.  1.823(a)(5)), with the number of separate sequences being equal 
in number to the number of continuous strings of sequence data. A 
sequence composed of one or more noncontiguous segments of a larger 
sequence or segments from different sequences shall be presented as a 
separate sequence.
0
12. Revise Sec.  1.823 to read as follows:


Sec.  1.823  Requirements for content of a ``Sequence Listing'' part of 
the specification.

    (a) The ``Sequence Listing'' must comply with the following:
    (1) The order and presentation of the items of information in the 
``Sequence Listing'' shall conform to the arrangement in Appendix G. 
The submission of those items of information designated with an ``M'' 
is mandatory. The submission of those items of information designated 
with an ``O'' is optional.
    (2) Each item of information shall begin on a new line with the 
numeric identifier enclosed in angle brackets, as shown in Appendix G.
    (3) Set forth numeric identifiers <110> through <170> at the 
beginning of the ``Sequence Listing.''
    (4) Include each disclosed nucleotide and/or amino acid sequence, 
as defined in Sec.  1.821(a).
    (5) Assign each sequence with a separate sequence identifier, 
beginning with 1 and increasing sequentially by integers, and include 
the sequence identifier in numeric identifier <210>.
    (6) Use the code ``000'' in place of the sequence where no sequence 
is present for a sequence identifier.
    (7) Include the total number of SEQ ID NOs in numeric identifier 
<160>, as defined in Appendix G, whether followed by a sequence or by 
the code ``000.''
    (8) Must not contain more than 74 characters per line.
    (b)(1) Unless paragraph (b)(2) of this section applies, if the 
``Sequence Listing'' required by Sec.  1.821(c) is submitted as an 
ASCII plain text file via the USPTO patent electronic filing system or 
on a read-only optical disc, in compliance with Sec.  1.52(e), then the 
specification must contain a statement in a separate paragraph (see 
Sec.  1.77(b)(5)) that incorporates by reference the material in the 
ASCII plain text file identifying:
    (i) The name of the file;
    (ii) The date of creation; and
    (iii) The size of the file in bytes.
    (2) If the ``Sequence Listing'' required by Sec.  1.821(c) is 
submitted as an ASCII plain text file via the USPTO patent electronic 
filing system or on a read-only optical disc, in compliance with Sec.  
1.52(e) for an international application during the international 
stage, then incorporation by reference of the material in the ASCII 
plain text file is not required.
    (3) A ``Sequence Listing'' required by Sec.  1.821(c) that is 
submitted as a PDF file (Sec.  1.821(c)(2)) via the USPTO patent 
electronic filing system or on physical sheets of paper (Sec.  
1.821(c)(3)), setting forth the nucleotide and/or amino acid sequence 
and associated information in accordance with paragraph (a) of this 
section:
    (i) Must begin on a new page;
    (ii) Must be titled ``Sequence Listing'';
    (iii) Must not include material other than the ``Sequence Listing'' 
itself;
    (iv) Must have sheets containing no more than 66 lines, with each 
line containing no more than 74 characters;
    (v) Should have sheets numbered independently of the numbering of 
the remainder of the application; and
    (vi) Should use a fixed-width font exclusively throughout.
0
13. Revise Sec.  1.824 to read as follows:


Sec.  1.824  Form and format for a nucleotide and/or amino acid 
sequence submission as an ASCII plain text file.

    (a) A ``Sequence Listing'' under Sec.  1.821(c)(1) and the CRF 
required by Sec.  1.821(e) submitted as an ASCII plain text file may be 
created by any means, such as text editors, nucleotide/amino acid 
sequence editors, or other custom computer programs; however, the ASCII 
plain text file must conform to the following requirements:
    (1) Must have the following compatibilities:
    (i) Computer compatibility: PC or Mac[supreg];
    (ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg].
    (2) Must be in ASCII plain text, where:
    (i) All printable characters (including the space character) are 
permitted;
    (ii) No nonprintable (ASCII control) characters are permitted, 
except ASCII CRLF or LF as line terminators.
    (3) Must be named as *.txt, where ``*'' is one character or a 
combination of characters limited to upper- or lowercase letters, 
numbers, hyphens, and underscores and does not exceed 60 characters in 
total, excluding the extension. No spaces or other types of characters 
are permitted in the file name.
    (4) Must contain no more than 74 printable characters in each line.
    (5) Pagination is not permitted; the ASCII plain text file must be 
one continuous file, with no ``hard page break'' codes and no page 
numbering.
    (b) The ASCII plain text file must contain a copy of a single 
``Sequence Listing'' in a single file and be submitted either:
    (1) Electronically via the USPTO patent electronic filing system, 
where the file must not exceed 100 MB, and file compression is not 
permitted; or
    (2) On read-only optical disc(s) in compliance with Sec.  1.52(e), 
where:
    (i) A file that is not compressed must be contained on a single 
read-only optical disc;
    (ii) The file may be compressed using WinZip[supreg], 7-Zip, or 
Unix[supreg]/Linux[supreg] Zip;
    (iii) A compressed file must not be self-extracting; and
    (iv) A compressed ASCII plain text file that does not fit on a 
single read-only optical disc may be split into multiple file parts, in 
accordance with the target read-only optical disc size, and labeled in 
compliance with 1.52(e)(5)(vi).
0
14. Revise Sec.  1.825 to read as follows:


Sec.  1.825  Amendment to add or replace a ``Sequence Listing'' and CRF 
copy thereof.

    (a) Any amendment adding a ``Sequence Listing'' (Sec.  1.821(c)) 
after the application filing date must include:
    (1) A ``Sequence Listing,'' in accordance with the requirements of 
Sec. Sec.  1.821 through 1.824, submitted as:
    (i) An ASCII plain text file under Sec.  1.821(c)(1) via the USPTO 
patent electronic filing system or on a read-only optical disc, in 
compliance with Sec.  1.52(e);
    (ii) PDF file via the USPTO patent electronic filing system; or
    (iii) Physical sheets of paper;
    (2) A request that the amendment be made:
    (i) By incorporation by reference of the material in the ASCII 
plain text file, in a separate paragraph of the specification, 
identifying the name of the file, the date of creation, and the size of 
the file in bytes (see Sec.  1.77(b)(5)), for a ``Sequence Listing'' 
submitted under Sec.  1.821(c)(1), except when submitted to the United 
States International Preliminary Examining Authority for an 
international application; or
    (ii) By inserting, after the abstract of the disclosure, a 
``Sequence Listing''

[[Page 28317]]

submitted as a PDF file under Sec.  1.821(c)(2) or submitted on 
physical sheets of paper under Sec.  1.821(c)(3), except when submitted 
to the United States International Preliminary Examining Authority for 
an international application;
    (3) A statement that indicates the basis for the amendment, with 
specific references to particular parts of the application 
(specification, claims, drawings) for all sequence data in the 
``Sequence Listing'' in the application as originally filed;
    (4) A statement that the ``Sequence Listing'' includes no new 
matter;
    (5) A new or substitute CRF under Sec.  1.821(e), if:
    (i) The added ``Sequence Listing'' is submitted as a PDF file, 
under Sec.  1.821(c)(2), or on physical sheets of paper, under Sec.  
1.821(c)(3); and
    (ii) A CRF, under Sec.  1.821(e), was not submitted, not compliant 
with Sec.  1.824, or not the same as the ``Sequence Listing''; and
    (6) A statement that the sequence information contained in the CRF 
is the same as the sequence information contained in the added 
``Sequence Listing,'' if submitted as a PDF file, under Sec.  
1.821(c)(2), or on physical sheets of paper, under Sec.  1.821(c)(3).
    (b) Any amendment to a ``Sequence Listing'' (Sec.  1.821(c)) must 
include:
    (1) A replacement ``Sequence Listing,'' in accordance with the 
requirements of Sec. Sec.  1.821 through 1.824, submitted as:
    (i) An ASCII plain text file under Sec.  1.821(c)(1) via the USPTO 
patent electronic filing system, or on a read-only optical disc, in 
compliance with Sec.  1.52(e), labeled as ``REPLACEMENT MM/DD/YYYY'' 
(with the month, day, and year of creation indicated);
    (ii) A PDF file via the USPTO patent electronic filing system; or
    (iii) Physical sheets of paper;
    (2) A request that the amendment be made:
    (i) By incorporation by reference of the material in the ASCII 
plain text file, in a separate paragraph of the specification 
(replacing any prior such paragraph, as applicable) identifying the 
name of the file, the date of creation, and the size of the file in 
bytes (see Sec.  1.77(b)(5)) for a ``Sequence Listing'' under Sec.  
1.821(c)(1), except when submitted to the United States International 
Preliminary Examining Authority for an international application; or
    (ii) By placing, after the abstract of the disclosure, a ``Sequence 
Listing'' submitted as a PDF file, under Sec.  1.821(c)(2), or on 
physical sheets of paper, under Sec.  1.821(c)(3) (replacing any prior 
``Sequence Listing,'' as applicable), except when submitted to the 
United States International Preliminary Examining Authority for an 
international application;
    (3) A statement that identifies the location of all deletions, 
replacements, or additions to the ``Sequence Listing'';
    (4) A statement that indicates the basis for the amendment, with 
specific references to particular parts of the application 
(specification, claims, drawings) as originally filed for all amended 
sequence data in the replacement ``Sequence Listing'';
    (5) A statement that the replacement ``Sequence Listing'' includes 
no new matter;
    (6) A new or substitute CRF under Sec.  1.821(e) with the amendment 
incorporated therein, if:
    (i) The replacement ``Sequence Listing'' is submitted as a PDF 
file, under Sec.  1.821(c)(2), or on physical sheets of paper, under 
Sec.  1.821(c)(3); and
    (ii) A CRF, under Sec.  1.821(e), was not submitted, not compliant 
with Sec.  1.824, or not the same as the submitted ``Sequence 
Listing''; and
    (7) A statement that the sequence information contained in the CRF 
is the same as the sequence information contained in the replacement 
``Sequence Listing'' when submitted as a PDF file, under Sec.  
1.821(c)(2), or on physical sheets of paper, under Sec.  1.821(c)(3).
    (c) The specification of a complete application, filed on the 
application filing date, with a ``Sequence Listing'' as an ASCII plain 
text file, under Sec.  1.821(c)(1), without an incorporation by 
reference of the material contained in the ASCII plain text file, must 
be amended to contain a separate paragraph incorporating by reference 
the material contained in the ASCII plain text file, in accordance with 
Sec.  1.77(b)(5), except for international applications during the 
international stage or national stage.
    (d) Any appropriate amendments to the ``Sequence Listing'' in a 
patent (e.g., by reason of reissue, reexamination, or certificate of 
correction) must comply with the requirements of paragraph (b) of this 
section.
0
15. Redesignate the appendix to subpart G of part 1 as appendix G, add 
appendices A through F, and revise newly redesignated appendix G as 
follows:

Appendices A Through G of Subpart G of Part 1

Appendix A: List of Nucleotides

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009)

------------------------------------------------------------------------
                                                           Origin of
             Symbol                     Meaning           designation
------------------------------------------------------------------------
a...............................  a.................  adenine.
g...............................  g.................  guanine.
c...............................  c.................  cytosine.
t...............................  t.................  thymine.
u...............................  u.................  uracil.
r...............................  g or a............  purine
y...............................  t/u or c..........  pyrimidine.
m...............................  a or c............  amino.
k...............................  g or t/u..........  keto.
s...............................  g or c............  strong
                                                       interactions 3H-
                                                       bonds.
w...............................  a or t/u..........  weak interactions
                                                       2H-bonds.
b...............................  g or c or t/u.....  not a.
d...............................  a or g or t/u.....  not c.
h...............................  a or c or t/u.....  not g.
v...............................  a or g or c.......  not t, not u.
n...............................  a or g or c or t/   any
                                   u, unknown, or
                                   other.
------------------------------------------------------------------------


[[Page 28318]]

Appendix B: List of Modified Nucleotides

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009)

------------------------------------------------------------------------
              Symbol                               Meaning
------------------------------------------------------------------------
ac4c..............................  4-acetylcytidine.
chm5u.............................  5-(carboxyhydroxymethyl)uridine.
cm................................  2'-O-methylcytidine.
cmnm5s2u..........................  5-carboxymethylaminomethyl-2-
                                     thiouridine.
cmnm5u............................  5-carboxymethylaminomethyluridine.
d.................................  dihydrouridine.
fm................................  2'-O-methylpseudouridine.
gal q.............................  beta, D-galactosylqueuosine.
gm................................  2'-O-methylguanosine.
i.................................  inosine.
i6a...............................  N6-isopentenyladenosine.
m1a...............................  1-methyladenosine.
m1f...............................  1-methylpseudouridine.
m1g...............................  1-methylguanosine.
m1i...............................  1-methylinosine.
m22g..............................  2,2-dimethylguanosine.
m2a...............................  2-methyladenosine.
m2g...............................  2-methylguanosine.
m3c...............................  3-methylcytidine.
m5c...............................  5-methylcytidine.
m6a...............................  N6-methyladenosine.
m7g...............................  7-methylguanosine.
mam5u.............................  5-methylaminomethyluridine.
mam5s2u...........................  5-methoxyaminomethyl-2-thiouridine.
man q.............................  beta, D-mannosylqueuosine.
mcm5s2u...........................  5-methoxycarbonylmethyl-2-
                                     thiouridine.
mcm5u.............................  5-methoxycarbonylmethyluridine.
mo5u..............................  5-methoxyuridine.
ms2i6a............................  2-methylthio-N6-
                                     isopentenyladenosine.
ms2t6a............................  N-((9-beta-D-ribofuranosyl-2-
                                     methylthiopurine-6-
                                     yl)carbamoyl)threonine.
mt6a..............................  N-((9-beta-D-ribofuranosylpurine-6-
                                     yl)N-methylcarbamoyl)threonine.
mv................................  uridine-5-oxyacetic acid-
                                     methylester.
o5u...............................  uridine-5-oxyacetic acid.
osyw..............................  wybutoxosine.
p.................................  pseudouridine.
q.................................  queuosine.
s2c...............................  2-thiocytidine.
s2t...............................  5-methyl-2-thiouridine.
s2u...............................  2-thiouridine.
s4u...............................  4-thiouridine.
t.................................  5-methyluridine.
t6a...............................  N-((9-beta-D-ribofuranosylpurine-6-
                                     yl)-carbamoyl)threonine.
tm................................  2'-O-methyl-5-methyluridine.
um................................  2'-O-methyluridine.
yw................................  wybutosine.
x.................................  3-(3-amino-3-carboxy-propyl)uridine,
                                     (acp3)u.
------------------------------------------------------------------------

Appendix C: List of Amino Acids

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009)

------------------------------------------------------------------------
                  Symbol                               Meaning
------------------------------------------------------------------------
Ala.......................................  Alanine.
Cys.......................................  Cysteine.
Asp.......................................  Aspartic Acid.
Glu.......................................  Glutamic Acid.
Phe.......................................  Phenylalanine.
Gly.......................................  Glycine.
His.......................................  Histidine.
Ile.......................................  Isoleucine.
Lys.......................................  Lysine.
Leu.......................................  Leucine.
Met.......................................  Methionine.
Asn.......................................  Asparagine.
Pro.......................................  Proline.
Gln.......................................  Glutamine.
Arg.......................................  Arginine.
Ser.......................................  Serine.
Thr.......................................  Threonine.
Val.......................................  Valine.
Trp.......................................  Tryptophan.
Tyr.......................................  Tyrosine.
Asx.......................................  Asp or Asn.
Glx.......................................  Glu or Gln.
Xaa.......................................  unknown or other.
------------------------------------------------------------------------

Appendix D: List of Modified and Unusual Amino Acids

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009)

------------------------------------------------------------------------
                  Symbol                               Meaning
------------------------------------------------------------------------
Aad.......................................  2-Aminoadipic acid.
bAad......................................  3-Aminoadipic acid.
bAla......................................  beta-Alanine, beta-
                                             Aminopropionic acid.
Abu.......................................  2-Aminobutyric acid.

[[Page 28319]]

 
4Abu......................................  4-Aminobutyric acid,
                                             piperidinic acid.
Acp.......................................  6-Aminocaproic acid.
Ahe.......................................  2-Aminoheptanoic acid.
Aib.......................................  2-Aminoisobutyric acid.
bAib......................................  3-Aminoisobutyric acid.
Apm.......................................  2-Aminopimelic acid.
Dbu.......................................  2,4 Diaminobutyric acid.
Des.......................................  Desmosine.
Dpm.......................................  2,2'-Diaminopimelic acid.
Dpr.......................................  2,3-Diaminopropionic acid.
EtGly.....................................  N-Ethylglycine.
EtAsn.....................................  N-Ethylasparagine.
Hyl.......................................  Hydroxylysine.
aHyl......................................  allo-Hydroxylysine.
3Hyp......................................  3-Hydroxyproline.
4Hyp......................................  4-Hydroxyproline.
Ide.......................................  Isodesmosine.
aIle......................................  allo-Isoleucine.
MeGly.....................................  N-Methylglycine, sarcosine.
MeIle.....................................  N-Methylisoleucine.
MeLys.....................................  6-N-Methyllysine.
MeVal.....................................  N-Methylvaline.
Nva.......................................  Norvaline.
Nle.......................................  Norleucine.
Orn.......................................  Ornithine.
------------------------------------------------------------------------

Appendix E: List of Feature Keys Related to Nucleotide Sequences

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009)

------------------------------------------------------------------------
             Key                              Description
------------------------------------------------------------------------
allele.......................  a related individual or strain contains
                                stable, alternative forms of the same
                                gene, which differs from the presented
                                sequence at this location (and perhaps
                                others).
attenuator...................  (1) region of DNA at which regulation of
                                termination of transcription occurs,
                                which controls the expression of some
                                bacterial operons; (2) sequence segment
                                located between the promoter and the
                                first structural gene that causes
                                partial termination of transcription.
C_region.....................  constant region of immunoglobulin light
                                and heavy chains, and T-cell receptor
                                alpha, beta, and gamma chains; includes
                                one or more exons depending on the
                                particular chain.
CAAT_signal..................  CAAT box; part of a conserved sequence
                                located about 75 bp upstream of the
                                start point of eukaryotic transcription
                                units which may be involved in RNA
                                polymerase binding; consensus=GG (C or
                                T) CAATCT.
CDS..........................  coding sequence; sequence of nucleotides
                                that corresponds with the sequence of
                                amino acids in a protein (location
                                includes stop codon); feature includes
                                amino acid conceptual translation.
conflict.....................  independent determinations of the
                                ``same'' sequence differ at this site or
                                region.
D-loop.......................  displacement loop; a region within
                                mitochondrial DNA in which a short
                                stretch of RNA is paired with one strand
                                of DNA, displacing the original partner
                                DNA strand in this region; also used to
                                describe the displacement of a region of
                                one strand of duplex DNA by a single
                                stranded invader in the reaction
                                catalyzed by RecA protein.
D-segment....................  diversity segment of immunoglobulin heavy
                                chain, and T-cell receptor beta chain.
enhancer.....................  a cis-acting sequence that increases the
                                utilization of (some) eukaryotic
                                promoters, and can function in either
                                orientation and in any location
                                (upstream or downstream) relative to the
                                promoter.
exon.........................  region of genome that codes for portion
                                of spliced mRNA; may contain 5'UTR, all
                                CDSs, and 3'UTR.
GC_signal....................  GC box; a conserved GC-rich region
                                located upstream of the start point of
                                eukaryotic transcription units which may
                                occur in multiple copies or in either
                                orientation; consensus=GGGCGG.
gene.........................  region of biological interest identified
                                as a gene and for which a name has been
                                assigned.
iDNA.........................  intervening DNA; DNA which is eliminated
                                through any of several kinds of
                                recombination.
intron.......................  a segment of DNA that is transcribed, but
                                removed from within the transcript by
                                splicing together the sequences (exons)
                                on either side of it.
J_segment....................  joining segment of immunoglobulin light
                                and heavy chains, and T-cell receptor
                                alpha, beta, and gamma chains.
LTR..........................  long terminal repeat, a sequence directly
                                repeated at both ends of a defined
                                sequence, of the sort typically found in
                                retroviruses.
mat_peptide..................  mature peptide or protein coding
                                sequence; coding sequence for the mature
                                or final peptide or protein product
                                following post-translational
                                modification; the location does not
                                include the stop codon (unlike the
                                corresponding CDS).
misc_binding.................  site in nucleic acid which covalently or
                                non-covalently binds another moiety that
                                cannot be described by any other Binding
                                key (primer_bind or protein_bind).
misc_difference..............  feature sequence is different from that
                                presented in the entry and cannot be
                                described by any other Difference key
                                (conflict, unsure, old_sequence,
                                mutation, variation, allele, or
                                modified_base).
misc_feature.................  region of biological interest which
                                cannot be described by any other feature
                                key; a new or rare feature.
misc_recomb..................  site of any generalized, site-specific or
                                replicative recombination event where
                                there is a breakage and reunion of
                                duplex DNA that cannot be described by
                                other recombination keys (iDNA and
                                virion) or qualifiers of source key (/
                                insertion_seq, /transposon, /proviral).
misc_RNA.....................  any transcript or RNA product that cannot
                                be defined by other RNA keys
                                (prim_transcript, precursor_RNA, mRNA,
                                5'clip, 3'clip, 5'UTR, 3'UTR, exon, CDS,
                                sig_peptide, transit_peptide,
                                mat_peptide, intron, polyA_site, rRNA,
                                tRNA, scRNA, and snRNA).
misc_signal..................  any region containing a signal
                                controlling or altering gene function or
                                expression that cannot be described by
                                other Signal keys (promoter,
                                CAAT_signal, TATA_signal, -35_signal, -
                                10_signal, GC_signal, RBS, polyA_signal,
                                enhancer, attenuator, terminator, and
                                rep_origin).
misc_structure...............  any secondary or tertiary structure or
                                conformation that cannot be described by
                                other Structure keys (stem_loop and D-
                                loop).
modified_base................  the indicated nucleotide is a modified
                                nucleotide and should be substituted for
                                by the indicated molecule (given in the
                                mod_base qualifier value).
mRNA.........................  messenger RNA; includes 5' untranslated
                                region (5'UTR), coding sequences (CDS,
                                exon) and 3' untranslated region
                                (3'UTR).
mutation.....................  a related strain has an abrupt,
                                inheritable change in the sequence at
                                this location.
N_region.....................  extra nucleotides inserted between
                                rearranged immunoglobulin segments.
old_sequence.................  the presented sequence revises a previous
                                version of the sequence at this
                                location.
polyA_signal.................  recognition region necessary for
                                endonuclease cleavage of an RNA
                                transcript that is followed by
                                polyadenylation; consensus=AATAAA.
polyA_site...................  site on an RNA transcript to which will
                                be added adenine residues by post-
                                transcriptional polyadenylation.

[[Page 28320]]

 
precursor_RNA................  any RNA species that is not yet the
                                mature RNA product; may include 5'
                                clipped region (5'clip), 5' untranslated
                                region (5'UTR), coding sequences (CDS,
                                exon), intervening sequences (intron),
                                3' untranslated region (3'UTR), and 3'
                                clipped region (3'clip).
prim_transcript..............  primary (initial, unprocessed)
                                transcript; includes 5' clipped region
                                (5'clip), 5' untranslated region
                                (5'UTR), coding sequences (CDS, exon),
                                intervening sequences (intron), 3'
                                untranslated region (3'UTR), and 3'
                                clipped region (3'clip).
primer_bind..................  non-covalent primer binding site for
                                initiation of replication,
                                transcription, or reverse transcription;
                                includes site(s) for synthetic, for
                                example, PCR primer elements.
promoter.....................  region on a DNA molecule involved in RNA
                                polymerase binding to initiate
                                transcription.
protein_bind.................  non-covalent protein binding site on
                                nucleic acid.
RBS..........................  ribosome binding site.
repeat_region................  region of genome containing repeating
                                units.
repeat_unit..................  single repeat element.
rep_origin...................  origin of replication; starting site for
                                duplication of nucleic acid to give two
                                identical copies.
rRNA.........................  mature ribosomal RNA; the RNA component
                                of the ribonucleoprotein particle
                                (ribosome) which assembles amino acids
                                into proteins.
S_region.....................  switch region of immunoglobulin heavy
                                chains; involved in the rearrangement of
                                heavy chain DNA leading to the
                                expression of a different immunoglobulin
                                class from the same B-cell.
satellite....................  many tandem repeats (identical or
                                related) of a short basic repeating
                                unit; many have a base composition or
                                other property different from the genome
                                average that allows them to be separated
                                from the bulk (main band) genomic DNA.
scRNA........................  small cytoplasmic RNA; any one of several
                                small cytoplasmic RNA molecules present
                                in the cytoplasm and (sometimes) nucleus
                                of a eukaryote.
sig_peptide..................  signal peptide coding sequence; coding
                                sequence for an N-terminal domain of a
                                secreted protein; this domain is
                                involved in attaching nascent
                                polypeptide to the membrane; leader
                                sequence.
snRNA........................  small nuclear RNA; any one of many small
                                RNA species confined to the nucleus;
                                several of the snRNAs are involved in
                                splicing or other RNA processing
                                reactions.
source.......................  identifies the biological source of the
                                specified span of the sequence; this key
                                is mandatory; every entry will have, as
                                a minimum, a single source key spanning
                                the entire sequence; more than one
                                source key per sequence is permissible.
stem_loop....................  hairpin; a double-helical region formed
                                by base-pairing between adjacent
                                (inverted) complementary sequences in a
                                single strand of RNA or DNA.
STS..........................  Sequence Tagged Site; short, single-copy
                                DNA sequence that characterizes a
                                mapping landmark on the genome and can
                                be detected by PCR; a region of the
                                genome can be mapped by determining the
                                order of a series of STSs.
TATA_signal..................  TATA box; Goldberg-Hogness box; a
                                conserved AT-rich septamer found about
                                25 bp before the start point of each
                                eukaryotic RNA polymerase II transcript
                                unit which may be involved in
                                positioning the enzyme for correct
                                initiation; consensus=TATA(A or T)A(A or
                                T).
terminator...................  sequence of DNA located either at the end
                                of the transcript or adjacent to a
                                promoter region that causes RNA
                                polymerase to terminate transcription;
                                may also be site of binding of repressor
                                protein.
transit_peptide..............  transit peptide coding sequence; coding
                                sequence for an N-terminal domain of a
                                nuclear-encoded organellar protein; this
                                domain is involved in post-translational
                                import of the protein into the
                                organelle.
tRNA.........................  mature transfer RNA, a small RNA molecule
                                (75-85 bases long) that mediates the
                                translation of a nucleic acid sequence
                                into an amino acid sequence.
unsure.......................  author is unsure of exact sequence in
                                this region.
V_region.....................  variable region of immunoglobulin light
                                and heavy chains, and T-cell receptor
                                alpha, beta, and gamma chains; codes for
                                the variable amino terminal portion; can
                                be made up from V_segments, D_segments,
                                N_regions, and J_segments.
V_segment....................  variable segment of immunoglobulin light
                                and heavy chains, and T-cell receptor
                                alpha, beta, and gamma chains; codes for
                                most of the variable region (V_region)
                                and the last few amino acids of the
                                leader peptide.
variation....................  a related strain contains stable
                                mutations from the same gene (for
                                example, RFLPs, polymorphisms, etc.)
                                which differ from the presented sequence
                                at this location (and possibly others).
3'clip.......................  3'-most region of a precursor transcript
                                that is clipped off during processing.
3'UTR........................  region at the 3' end of a mature
                                transcript (following the stop codon)
                                that is not translated into a protein.
5'clip.......................  5'-most region of a precursor transcript
                                that is clipped off during processing.
5'UTR........................  region at the 5' end of a mature
                                transcript (preceding the initiation
                                codon) that is not translated into a
                                protein.
-10_signal...................  pribnow box; a conserved region about 10
                                bp upstream of the start point of
                                bacterial transcription units which may
                                be involved in binding RNA polymerase;
                                consensus=TAtAaT.
-35_signal...................  a conserved hexamer about 35 bp upstream
                                of the start point of bacterial
                                transcription units; consensus=TTGACa [
                                ] or TGTTGACA [ ].
------------------------------------------------------------------------

Appendix F: List of Feature Keys Related to Protein Sequences

    Source: World Intellectual Property Organization (WIPO) Handbook 
on Industrial Property Information and Documentation, Standard 
ST.25: Standard for the Presentation of Nucleotide and Amino Acid 
Sequence Listings in Patent Applications (2009)

------------------------------------------------------------------------
                Key                              Description
------------------------------------------------------------------------
CONFLICT..........................  different papers report differing
                                     sequences.
VARIANT...........................  authors report that sequence
                                     variants exist.
VARSPLIC..........................  description of sequence variants
                                     produced by alternative splicing.

[[Page 28321]]

 
MUTAGEN...........................  site which has been experimentally
                                     altered.
MOD_RES...........................  post-translational modification of a
                                     residue.
ACETYLATION.......................  N-terminal or other.
AMIDATION.........................  generally at the C-terminal of a
                                     mature active peptide.
BLOCKED...........................  undetermined N- or C-terminal
                                     blocking group.
FORMYLATION.......................  of the N-terminal methionine.
GAMMA-CARBOXYGLUTAMIC ACID          of asparagine, aspartic acid,
 HYDROXYLATION.                      proline, or lysine.
METHYLATION.......................  generally of lysine or arginine.
PHOSPHORYLATION...................  of serine, threonine, tyrosine,
                                     aspartic acid or histidine.
PYRROLIDONE CARBOXYLIC ACID.......  N-terminal glutamate which has
                                     formed an internal cyclic lactam.
SULFATATION.......................  generally of tyrosine.
LIPID.............................  covalent binding of a lipidic
                                     moiety.
MYRISTATE.........................  myristate group attached through an
                                     amide bond to the N-terminal
                                     glycine residue of the mature form
                                     of a protein or to an internal
                                     lysine residue.
PALMITATE.........................  palmitate group attached through a
                                     thioether bond to a cysteine
                                     residue or through an ester bond to
                                     a serine or threonine residue.
FARNESYL..........................  farnesyl group attached through a
                                     thioether bond to a cysteine
                                     residue.
GERANYL-GERANYL...................  geranyl-geranyl group attached
                                     through a thioether bond to a
                                     cysteine residue.
GPI-ANCHOR........................  glycosyl-phosphatidylinositol (GPI)
                                     group linked to the alpha-carboxyl
                                     group of the C-terminal residue of
                                     the mature form of a protein.
N-ACYL DIGLYCERIDE................  N-terminal cysteine of the mature
                                     form of a prokaryotic lipoprotein
                                     with an amide-linked fatty acid and
                                     a glyceryl group to which two fatty
                                     acids are linked by ester linkages.
DISULFID..........................  disulfide bond; the `FROM' and `TO'
                                     endpoints represent the two
                                     residues which are linked by an
                                     intra-chain disulfide bond; if the
                                     `FROM' and `TO' endpoints are
                                     identical, the disulfide bond is an
                                     interchain one and the description
                                     field indicates the nature of the
                                     cross-link.
THIOLEST..........................  thiolester bond; the `FROM' and `TO'
                                     endpoints represent the two
                                     residues which are linked by the
                                     thiolester bond.
THIOETH...........................  thioether bond; the `FROM' and `TO'
                                     endpoints represent the two
                                     residues which are linked by the
                                     thioether bond.
CARBOHYD..........................  glycosylation site; the nature of
                                     the carbohydrate (if known) is
                                     given in the description field.
METAL.............................  binding site for a metal ion; the
                                     description field indicates the
                                     nature of the metal.
BINDING...........................  binding site for any chemical group
                                     (co-enzyme, prosthetic group,
                                     etc.); the chemical nature of the
                                     group is given in the description
                                     field.
SIGNAL............................  extent of a signal sequence
                                     (prepeptide).
TRANSIT...........................  extent of a transit peptide
                                     (mitochondrial, chloroplastic, or
                                     for a microbody).
PROPEP............................  extent of a propeptide.
CHAIN.............................  extent of a polypeptide chain in the
                                     mature protein.
PEPTIDE...........................  extent of a released active peptide.
DOMAIN............................  extent of a domain of interest on
                                     the sequence; the nature of that
                                     domain is given in the description
                                     field.
CA_BIND...........................  extent of a calcium-binding region.
DNA_BIND..........................  extent of a DNA-binding region.
NP_BIND...........................  extent of a nucleotide phosphate
                                     binding region; the nature of the
                                     nucleotide phosphate is indicated
                                     in the description field.
TRANSMEM..........................  extent of a transmembrane region.
ZN_FING...........................  extent of a zinc finger region.
SIMILAR...........................  extent of a similarity with another
                                     protein sequence; precise
                                     information, relative to that
                                     sequence, is given in the
                                     description field.
REPEAT............................  extent of an internal sequence
                                     repetition.
HELIX.............................  secondary structure: Helices, for
                                     example, Alpha-helix, 3(10) helix,
                                     or Pi-helix.
STRAND............................  secondary structure: Beta-strand,
                                     for example, Hydrogen bonded beta-
                                     strand, or Residue in an isolated
                                     beta-bridge.
TURN..............................  secondary structure Turns, for
                                     example, H-bonded turn (3-turn, 4-
                                     turn, or 5-turn).
ACT_SITE..........................  amino acid(s) involved in the
                                     activity of an enzyme.
SITE..............................  any other interesting site on the
                                     sequence.
INIT_MET..........................  the sequence is known to start with
                                     an initiator methionine.
NON_TER...........................  the residue at an extremity of the
                                     sequence is not the terminal
                                     residue; if applied to position 1,
                                     this signifies that the first
                                     position is not the N-terminus of
                                     the complete molecule; if applied
                                     to the last position, it signifies
                                     that this position is not the C-
                                     terminus of the complete molecule;
                                     there is no description field for
                                     this key.
NON_CONS..........................  non consecutive residues; indicates
                                     that two residues in a sequence are
                                     not consecutive and that there are
                                     a number of unsequenced residues
                                     between them.
UNSURE............................  uncertainties in the sequence; used
                                     to describe region(s) of a sequence
                                     for which the authors are unsure
                                     about the sequence assignment.
------------------------------------------------------------------------


[[Page 28322]]

Appendix G: Numeric Identifiers

----------------------------------------------------------------------------------------------------------------
                                                                                             Mandatory (M) or
          Numeric identifier                  Definition          Comments and format          optional (O)
----------------------------------------------------------------------------------------------------------------
<110>................................  Applicant..............  If Applicant is          M.
                                                                 inventor, then
                                                                 preferably max. of 10
                                                                 names; one name per
                                                                 line; preferable
                                                                 format: Surname, Other
                                                                 Names and/or Initials.
<120>................................  Title of Invention.....  .......................  M.
<130>................................  File Reference.........  Personal file reference  M when filed prior to
                                                                                          assignment or appl.
                                                                                          number.
<140>................................  Current Application      Specify as: US 09/       M, if available.
                                        Number.                  999,999 or PCT/US09/
                                                                 99999.
<141>................................  Current Filing Date....  Specify as: yyyy-mm-dd.  M, if available.
<150>................................  Prior Application        Specify as: US 09/       M, if applicable
                                        Number.                  999,999 or PCT/US09/     include priority
                                                                 99999.                   documents under 35
                                                                                          U.S.C. 119 and 120.
<151>................................  Prior Application        Specify as: yyyy-mm-dd.  M, if applicable.
                                        Filing Date.
<160>................................  Number of SEQ ID NOs...  Count includes total     M.
                                                                 number of SEQ ID NOs.
<170>................................  Software...............  Name of software used    O.
                                                                 to create the
                                                                 ``Sequence Listing.''.
<210>................................  SEQ ID NO:#:...........  Response shall be an     M.
                                                                 integer representing
                                                                 the SEQ ID NO shown.
<211>................................  Length.................  Respond with an integer  M.
                                                                 expressing the number
                                                                 of bases or amino acid
                                                                 residues.
<212>................................  Type...................  Whether presented        M.
                                                                 sequence molecule is
                                                                 DNA, RNA, or PRT
                                                                 (protein). If a
                                                                 nucleotide sequence
                                                                 contains both DNA and
                                                                 RNA fragments, the
                                                                 type shall be ``DNA.''
                                                                 In addition, the
                                                                 combined DNA/RNA
                                                                 molecule shall be
                                                                 further described in
                                                                 the <220> to <223>
                                                                 feature section.
<213>................................  Organism...............  Scientific name, i.e.    M.
                                                                 Genus/species, Unknown
                                                                 or Artificial
                                                                 Sequence. In addition,
                                                                 the ``Unknown'' or
                                                                 ``Artificial
                                                                 Sequence'' organisms
                                                                 shall be further
                                                                 described in the <220>
                                                                 to <223> feature
                                                                 section.
<220>................................  Feature................  Leave blank after        M, under the following
                                                                 <220>. <221-223>         conditions: if ``n,''
                                                                 provide for a            ``Xaa,'' or a modified
                                                                 description of points    or unusual L-amino
                                                                 of biological            acid or modified base
                                                                 significance in the      was used in a
                                                                 sequence.                sequence; if ORGANISM
                                                                                          is ``Artificial
                                                                                          Sequence'' or
                                                                                          ``Unknown''; if
                                                                                          molecule is combined
                                                                                          DNA/RNA.
<221>................................  Name/Key...............  Provide appropriate      M, under the following
                                                                 identifier for           conditions: if ``n,''
                                                                 feature, from WIPO       ``Xaa,'' or a modified
                                                                 Standard ST.25 (2009),   or unusual L-amino
                                                                 Appendices E and F to    acid or modified base
                                                                 this subpart.            was used in a
                                                                                          sequence.
<222>................................  Location...............  Specify location within  M, under the following
                                                                 sequence; where          conditions: if ``n,''
                                                                 appropriate, state       ``Xaa,'' or a modified
                                                                 number of first and      or unusual L-amino
                                                                 last bases/amino acids   acid or modified base
                                                                 in feature.              was used in a
                                                                                          sequence.
<223>................................  Other Information......  Other relevant           M, under the following
                                                                 information; four        conditions: if ``n,''
                                                                 lines maximum.           ``Xaa,'' or a modified
                                                                                          or unusual L-amino
                                                                                          acid or modified base
                                                                                          was used in a
                                                                                          sequence; if ORGANISM
                                                                                          is ``Artificial
                                                                                          Sequence'' or
                                                                                          ``Unknown''; if
                                                                                          molecule is combined
                                                                                          DNA/RNA.
<300>................................  Publication Information  Leave blank after <300>  O.
<301>................................  Authors................  Preferably max. of 10    O.
                                                                 named authors of
                                                                 publication; specify
                                                                 one name per line;
                                                                 preferable format:
                                                                 Surname, Other Names
                                                                 and/or Initials.
<302>................................  Title..................  .......................  O.
<303>................................  Journal................  .......................  O.
<304>................................  Volume.................  .......................  O.
<305>................................  Issue..................  .......................  O.
<306>................................  Pages..................  .......................  O.
<307>................................  Date...................  Journal date on which    O.
                                                                 data published;
                                                                 specify as yyyy-mm-dd,
                                                                 MMM-yyyy or Season-
                                                                 yyyy.
<308>................................  Database Accession       Accession number         O.
                                        Number.                  assigned by database,
                                                                 including database
                                                                 name.
<309>................................  Database Entry Date....  Date of entry in         O.
                                                                 database; specify as
                                                                 yyyy-mm-dd or MMM-yyyy.
<310>................................  Patent Document Number.  Document number; for     O.
                                                                 patent-type citations
                                                                 only. Specify as, for
                                                                 example, US 09/999,999.
<311>................................  Patent Filing Date.....  Document filing date,    O.
                                                                 for patent-type
                                                                 citations only;
                                                                 specify as yyyy-mm-dd.

[[Page 28323]]

 
<312>................................  Publication Date.......  Document publication     O.
                                                                 date, for patent-type
                                                                 citations only;
                                                                 specify as yyyy-mm-dd.
<313>................................  Relevant Residues......  FROM (position) TO       O.
                                                                 (position).
<400>................................  Sequence...............  SEQ ID NO should follow  M.
                                                                 the numeric identifier
                                                                 and should appear on
                                                                 the line preceding the
                                                                 actual sequence.
----------------------------------------------------------------------------------------------------------------


Andrew Hirshfeld,
Commissioner for Patents, Performing the Functions and Duties of the 
Under Secretary of Commerce for Intellectual Property and Director of 
the United States Patent and Trademark Office.
[FR Doc. 2021-10421 Filed 5-25-21; 8:45 am]
BILLING CODE 3510-16-P