[Federal Register Volume 63, Number 104 (Monday, June 1, 1998)]
[Rules and Regulations]
[Pages 29620-29643]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 98-14194]
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DEPARTMENT OF COMMERCE
Patent and Trademark Office
37 CFR Part 1
[Docket No: 960828235-8109-02]
RIN: 0651-AA88
Requirements for Patent Applications Containing Nucleotide
Sequence and/or Amino Acid Disclosures
AGENCY: Patent and Trademark Office, Commerce.
ACTION: Final rule.
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SUMMARY: The Patent and Trademark Office (PTO) is amending the rules
for submitting nucleotide or amino acid sequences in computer readable
form (CRF) for patent applications. These amendments simplify the
requirements of the rules, rearrange portions of the rules for better
understanding and establish consistent rules to permit a single
internationally acceptable computer readable form. Sequence Listings
will be presented in an international, language neutral format using
numeric identifiers rather than the current subject headings. The Paper
Sequence Listing will preferably be a separately numbered section of
the patent application. Sequences which contain fewer than four
specifically identified nucleotides or amino acids will no longer be
required to be submitted in computer readable form.
DATES: Effective date: July 1, 1998. The incorporation by reference of
certain publications listed in the regulations is approved by the
Director of the Federal Register as of July 1, 1998.
Applicability date: Sections 1.821 through 1.825 as amended apply
to applications filed on or after July 1, 1998, except for: (1)
applications that claim the benefit of a prior application under 35
U.S.C. 120 filed before July 1, 1998, and which do not add subject
matter involving a sequence listing subject to Secs. 1.821 through
1.825; and (2) reissue applications in which the application for the
patent sought to be reissued was filed before July 1, 1998. Sections
1.821 through 1.825 apply during a reexamination proceeding if the
application for the patent sought to be reexamined was filed on or
after July 1, 1998.
FOR FURTHER INFORMATION CONTACT: Esther M. Kepplinger, by telephone at
(703) 308-1495; by mail addressed to: Box Comments--Patents, Assistant
Commissioner for Patents, Washington, DC 20231 marked to her attention;
by facsimile to (703) 305-3935; or by electronic mail at
esther.kepplinger@uspto.gov.
SUPPLEMENTARY INFORMATION: Sections 1.821 through 1.825 of title 37
provide a standardized format for the description of nucleotide and
amino acid sequence data in patent applications and require the
submission of such sequences in computer readable form (CRF). Sections
1.821 through 1.825 provide the following benefits to the PTO: (1)
Improved search capabilities; (2) improved interference detection; (3)
more efficient examination; (4) cost savings for the input of the
sequence data; (5) more
[[Page 29621]]
efficient and accurate printing of sequences in patents; (6) exchange
of the sequence data with other patent offices electronically; and (7)
improved public access to the sequences electronically.
Reasons for the Changes
In response to the needs of our customers, the procedural
requirements found in former Secs. 1.821 through 1.825 have been
reduced. Sections 1.821 through 1.825 are being amended to be
consistent with World Intellectual Property Organization (WIPO)
Standard ST.25 (signed in 1998 and effective July 1, 1998). ST.25
replaces WIPO Standards ST.23 and ST.24 which deal with paper and
electronic submissions of sequence listings.
A Meeting of International Authorities (MIA) under the Patent
Cooperation Treaty (PCT) was held in November of 1994 to discuss
simplification of sequence listing submission requirements. Under the
previous PCT Regulations, each International Searching Authority, each
International Preliminary Examining Authority and each designated/
elected office was free to set the requirements for submission of
sequence listings in paper and electronic form. This imposed a burden
on applicants by requiring them to prepare sequence listings in many
different formats. In addition, sequence listings were required to be
translated for consideration in the national stage at considerable cost
to applicants and at the risk that the information could be
inaccurately translated.
After the November 1994 MIA, the PTO, the European Patent Office
(EPO) and the Japanese Patent Office (JPO) worked together with WIPO to
create a new international standard which forms the basis of WIPO
Standard ST.25 (1998). Sections 1.821 through 1.825 of 37 CFR, as
amended herein, are consistent with WIPO Standard ST.25 (1998) and the
PCT sequence listing requirements. Sequence listings prepared in
accordance with Secs. 1.821 through 1.825 as amended generally will be
acceptable in all countries which adhere to WIPO Standard ST.25 (1998).
In addition, a sequence listing prepared in accordance with the
Secs. 1.821 through 1.825 as amended will be acceptable for the
national stage in all PCT member countries which require the submission
of a sequence listing. As a result of this rule change, applicants will
experience a reduction in cost since only one sequence listing in paper
and electronic form will need to be prepared and translations of this
listing will not be needed.
All necessary changes to the text of Secs. 1.821 through 1.825 to
reflect the new WIPO Standard ST.25 (1998), have been made. Each change
is described below.
Overview of the Changes
The changes in this Final Rule include:
(1) Use of numeric identifiers to replace the language subject
headings within the submission;
(2) Elimination of unnecessary and confusing data elements;
(3) Movement of the paper Sequence Listing to the end of the
application, preferably with separately numbered pages;
(4) Elimination of the requirement to provide a submission for
sequences with fewer than four specifically defined nucleotides or
amino acids;
(5) Use of lower-case one-letter codes for nucleotide bases;
(6) Rearrangement of portions of the rules to improve their
context;
(7) Clarification and simplification of the rules to aid in
understanding; and
(8) Minor changes to accomplish harmonization with WIPO Standard
ST.25 (1998) as well as the EPO and the JPO standards.
Amended Secs. 1.821 through 1.825 are not mandatory for: (1)
applications that claim the benefit of a prior application under 35
U.S.C. 120 filed before July 1, 1998, and which do not add subject
matter involving a sequence listing subject to Secs. 1.821 through
1.825; (2) reissue applications in which the application for the patent
sought to be reissued was filed before July 1, 1998; and (3)
reexamination proceedings if the application for the patent sought to
be reexamined was filed before July 1, 1998. The PTO will accept and
encourages the submission of sequence listings in compliance with
amended Secs. 1.821 through 1.825 for any application or reexamination
proceeding. All sequence listings (including the entire computer
readable form) must be submitted in compliance with either Secs. 1.821
through 1.825 as amended in this Final Rule or (when permitted) former
Secs. 1.821 through 1.825.
If the CRF for a new application would be identical to a compliant
CRF already on file in the PTO, the applicant may make reference to the
other application and the CRF in lieu of filing a duplicate CRF in the
new application by following the procedures set forth in Sec. 1.821(e).
If exceptional circumstances do arise and certain applicants experience
specific hardships in attempting to comply with amended Secs. 1.821
through 1.825, the PTO will consider a petition under Sec. 1.183 to
waive certain requirements of Secs. 1.821 through 1.825.
A Notice of Proposed Rulemaking entitled ``Changes Implementing
Nucleotide and/or Amino Acid Sequence Listings'' (Notice of Proposed
Rulemaking) was published in the Federal Register at 61 FR 51855
(October 4, 1996), and in the Official Gazette of the Patent and
Trademark Office, at 1191 Off. Gaz. Pat. Office 168 (October 29, 1996).
Sections 1.821 through 1.825 as adopted contain several changes from
these sections. This Final Rule provides a discussion of the content of
the specific rules being amended, description of the changes in the
text of the proposed rules, and explanation of the reasons supporting
the changes. In addition, comments received in response to the Notice
of Proposed Rulemaking are analyzed.
Discussion of Specific Rules and Changes from the Proposed Rules:
Title 37 of the Code of Federal Regulations, Part 1, is amended as
follows.
Section 1.77
The proposed change to 37 CFR 1.77 was previously adopted. See
Miscellaneous Changes to Patent Practice; Final Rule, 61 FR 42790
(August 19, 1996), 1190 Off. Gaz. Pat. Office 67 (September 17, 1996).
Section 1.821
Section 1.821 incorporates by reference the World Intellectual
Property Organization (WIPO) Handbook on Industrial Property
Information and Documentation, Standard ST.25 (1998), including Tables
1 through 6 of Appendix 2, in accordance with 5 U.S.C. 552(a) and 1 CFR
part 51. Copies may be obtained from the World Intellectual Property
Organization; 34 chemin des Colombettes; 1211 Geneva 20 Switzerland.
Copies may be inspected at the Patent Search Room; Crystal Plaza 3,
Lobby Level; 2021 South Clark Place; Arlington, VA 22202. Copies may
also be inspected at the Office of the Federal Register, 800 North
Capitol Street, NW, Suite 700, Washington, DC 20408. These Tables are
reproduced below.
WIPO Standard ST.25 (1998), Appendix 2, Table 1, provides that the
bases of a nucleotide sequence should be represented using the
following one-letter code for nucleotide sequence characters:
[[Page 29622]]
Table 1.--One Letter Codes for Nucleotide Sequences
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Symbol Meaning Origin of designation
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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 3 H-bonds.
w................................... a or t/u............... weak interactions 2 H-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/u) or any
(unknown or other).
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WIPO Standard ST.25 (1998), Appendix 2, Table 2, provides that
modified bases may be represented as the corresponding unmodified bases
in the sequence itself, if the modified base is one of those listed
below and the modification is further described in the Feature section
of the Sequence Listing. The codes from the list below may be used in
the description (i.e., the specification and drawings, or in the
Sequence Listing) but these codes may not be used in the sequence
itself.
Table 2.--Modified Bases
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Symbol Meaning
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ac4c......................... 4-acetylcytidine.
chm5u........................ 5-(carboxyhydroxylmethyl)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.
[[Page 29623]]
yw........................... wybutosine.
x............................ 3-(3-amino-3-carboxy-propyl)uridine,
(acp3)u.
------------------------------------------------------------------------
WIPO Standard ST.25 (1998), Appendix 2, Table 3, provides that the
amino acids should be represented using the following three-letter code
with the first letter as a capital.
Table 3.--Amino Acid Three-Letter Codes
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Symbol Meaning
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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.
------------------------------------------------------------------------
WIPO Standard ST.25 (1998), Appendix 2, Table 4, provides that
modified and unusual amino acids may be represented as the
corresponding unmodified amino acids in the sequence itself if the
modified or unusual amino acid is one of those listed below and the
modification is further described in the Feature section of the
Sequence Listing. The codes from the list below may be used in the
description (i.e., the specification and drawings, or in the Sequence
Listing) but these codes may not be used in the sequence itself.
Table 4.--Modified and Unusual Amino Acid Codes
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Symbol Meaning
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Aad........................................ 2-Aminoadipic acid.
bAad....................................... 3-aminoadipic acid.
bAla....................................... beta-Alanine, beta-Aminopropionic acid.
Abu........................................ 2-Aminobutyric acid.
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.
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WIPO Standard ST.25 (1998), Appendix 2, Table 5 provides for
feature keys related to DNA sequences.
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Further in paragraph (a) of Sec. 1.821, both occurrences of
``Copies of ST.23'' have been changed to ``Copies of WIPO Standard
ST.25 (1998).'' This change is necessary to reflect the new standard
number.
In paragraph (a)(1) of Sec. 1.821, ``ST.23 (April 1994), paragraph
8'' has been changed to ``ST.25 (1998), Appendix 2, Table 1.'' This
change reflects the correct information with regard to the incorporated
WIPO standard and the list of symbols to be used for nucleotide
sequence characters.
Further in paragraph (a)(1) of Sec. 1.821, ``ST.23 (April 1994),
paragraph 9'' has been changed to ``ST.25 (1998), Appendix 2, Table
2.'' This change reflects the correct information with regard to the
incorporated WIPO standard and the list of modified bases which can be
presented as unmodified nucleotide sequence characters.
In paragraph (a)(2) of Sec. 1.821, all three occurrences of ``ST.23
(April 1994), paragraph 11'' have been changed to ``ST.25 (1998),
Appendix 2, Table 3.'' This change reflects the correct information
with regard to the incorporated WIPO standard and the list of symbols
to be used for amino acid sequence characters.
Further in paragraph (a)(2) of Sec. 1.821, ``ST.23 (April 1994),
paragraph 12'' has been changed to ``ST.25 (1998), Appendix 2, Table
4.'' This change reflects the correct information with regard to the
incorporated WIPO standard and the list of modified or unusual amino
acids which can be presented as unmodified amino acid sequence
characters.
In paragraph (c) of Sec. 1.821, each of the three occurrences of
the words ``integer identifier'' or ``integer identifiers'' has been
changed to ``sequence identifier'' or ``sequence identifiers'' as
appropriate. WIPO Standard ST.25 (1998), uses the term ``sequence
identifier'' rather than ``integer identifier.'' Thus, this change is
necessary to achieve harmonization with the international standard.
In the last sentence of paragraph (c) of Sec. 1.821, the phrase
``The sequence omitted shall appear following the integer identifier''
of the proposed rule has been replaced by ``the code `000' shall be
used in place of the sequence.'' The response for the numeric
identifier <160> shall include the total number of SEQ ID NOs, whether
followed by a sequence or by the code ``000''. The code ``000'' should
be put into <400>. This change permits flexibility in the preparation
and amendment of Sequence Listings. It also makes the rule language-
neutral and is consistent with WIPO Standard ST.25 (1998).
In paragraph (d) of Sec. 1.821, the words ``integer identifier''
have been changed to ``sequence identifier.'' WIPO Standard ST.25
(1998) uses the term ``sequence identifier'' rather than ``integer
identifier.'' Thus, this change is necessary to achieve harmonization
with the international standard.
In paragraphs (f), (g) and (h) of Sec. 1.821, the sentence ``Such a
statement must be a verified statement if made by a person not
registered to practice before the Office'' has been deleted. The
separate verification requirements in Sec. 1.821 have been eliminated
in view of the recent amendment to Secs. 1.4(d) and 10.18. See Changes
to Patent Practice and Procedure; Final Rule, 62 FR. 53131 (October 10,
1997), 1203 Off. Gaz. Pat. Office 63 (October 21, 1997). Paragraph (g)
of Sec. 1.821 has also been amended to provide that the Office will
provide a ``period of time'' (rather than one month) within which the
applicant must comply with the requirements of Sec. 1.821(b) through
(f) in order to avoid abandonment.
Further in paragraph (f) of Sec. 1.821, the following has been
added at the end of the first sentence, '', e.g., the information
recorded in computer readable form is identical to the written sequence
listing.'' WIPO Standard ST.25 (1998), paragraph 39, requires the
language which has been added as an acceptable example for phrasing the
required statement that the computer readable form and the written
sequence listing are the same.
Section 1.822
In paragraph (b) of Sec. 1.822, both references to WIPO Standard
ST.23 (April 1994), paragraphs 8 and 11, as proposed have been changed
to ``WIPO Standard ST.25 (1998), Appendix 2, Tables 1 and 3.'' These
changes reflect the correct information with regard to the incorporated
WIPO standard and the lists of symbols for nucleotide and amino acid
sequence characters.
Further in paragraph (b) of Sec. 1.822, ``WIPO Standard ST.23
(April 1994), paragraphs 9 and 12'' as proposed has been changed to
``WIPO Standard ST.25 (1998), Appendix 2, Tables 2 and 4.''
[[Page 29630]]
This change reflects the correct information with regard to the
incorporated WIPO standard and the lists of modified bases and modified
or unusual amino acids which can be depicted in the Sequence Listing
via the symbols for a corresponding unmodified base or amino acid.
Further in paragraph (b) of Sec. 1.822, the symbol designating an
unknown nucleotide base or a nucleotide base other than those listed in
the WIPO standard was proposed as an upper case letter ``N.'' This
symbol has been changed to a lower case letter ``n.'' This change is
consistent with the use of lower case letters for the symbols
representing the nucleotide bases.
Further in paragraph (b) of Sec. 1.822, the language has been
clarified to specifically state that each ``n'' or ``Xaa'' represents
only a single residue. Thus, for example, a single ``Xaa'' may not be
used to designate a string of four amino acids, each of which is
unknown. This represents a codification of existing practice.
Further in paragraph (b) of Sec. 1.822, the information required in
the Feature section to explain the use of ``n'' or ``Xaa'' in a given
sequence is referred to ``as appropriate.'' Additional instruction is
added at the end of paragraph (b) of Sec. 1.822 following ``the Feature
section'' indicating'', preferably by including one or more feature
keys listed in WIPO Standard ST.25 (1998), Appendix 2, Tables 5 and
6.'' This change specifies the preference for using the feature keys
listed in the WIPO standard in order to aid applicants in filing a CRF
which will comply with WIPO Standard ST.25 (1998). These feature keys
are controlled vocabulary and are considered language neutral. Their
use is required in a PCT patent application or a patent application in
a foreign country which has adopted WIPO Standard ST.25 (1998).
In paragraph (c)(1) of Sec. 1.822, ``WIPO Standard ST.23 (April
1994), paragraph 8'' as proposed has been changed to ``WIPO Standard
ST.25 (1998), Appendix 2, Table 1.'' This change reflects the correct
information with regard to the incorporated WIPO standard and the list
of symbols to be used for nucleotide sequence characters.
In paragraph (d)(1) of Sec. 1.822, ``WIPO Standard ST.23 (April
1994), paragraph 11, as proposed has been changed to ``WIPO Standard
ST.25 (1998), Appendix 2, Table 3.'' This change reflects the correct
information with regard to the incorporated WIPO standard and the list
of symbols to be used for amino acid sequence characters.
In paragraph (d)(4) of Sec. 1.822, the section notes that
enumeration requirements are applicable to amino acid sequences that
are circular in configuration. The following language has been added to
the end of the paragraph '', with the exception that the designation of
the first amino acid of the sequence may be made at the option of the
applicant.'' This change is necessary to provide consistency with its
counterpart of circular nucleotide sequences as provided in paragraph
(c)(7) of Sec. 1.822. This change is also consistent with WIPO Standard
ST.25 (1998), paragraph 21.
In paragraph (e) of Sec. 1.822, the words ``integer identifiers''
have been changed to ``sequence identifiers .'' WIPO Standard ST.25
(1998) uses the term ``sequence identifier'' rather than ``integer
identifier.'' Thus, this change is necessary to achieve harmonization
with the international standard.
Section 1.823
In paragraph (a) of Sec. 1.823, the entire second sentence which
read ``On a separate page of the application specification, immediately
prior to the claims, there shall be a reference to the presence of the
`Sequence Listing' in a `Sequence Listing Annex.''' has been
eliminated. The designation of the Sequence Listing as an annex to the
specification was initially proposed in an early version of the
international standard. This terminology is not used in WIPO Standard
ST.25 (1998), however, and so it has also been eliminated from
paragraph (a) of Sec. 1.823, as proposed. Simplification results as
well by the elimination of the requirement that the Sequence Listing
must be designated as an annex to the specification.
In paragraph (a) of Sec. 1.823, the third sentence has been
modified by deleting the words ``shall appear in the `Sequence Listing
Annex,' which is.'' As explained above, the current version of the
international standard does not require designating the Sequence
Listing as an annex to the specification.
In paragraph (a) of Sec. 1.823, the words ``preferably should be''
have been added to the third sentence, before ``numbered independently
of the numbering of the remainder of the application'' to describe the
independent page numbering of the Sequence Listing in paper copy form.
The term ``preferably'' was added for purposes of harmonization with
WIPO Standard ST.25 (1998).
In paragraph (a) of Sec. 1.823, the last clause of the third
sentence ``and shall be placed in the application file'' has been
deleted as unnecessary and potentially confusing now that the reference
to a ``Sequence Listing Annex'' has been removed from this paragraph.
In paragraph (a) of Sec. 1.823, the fourth sentence has been
eliminated in its entirety. As explained above, the current version of
the international standard does not require designating the Sequence
Listing as an annex to the specification.
In paragraph (a) of Sec. 1.823, in both occurrences in the fifth
sentence and in the single occurrence in the sixth sentence, the word
``shall'' has been changed to ``should.'' These changes are necessary
for purposes of achieving consistency with WIPO Standard ST.25 (1998).
In paragraph (b) of Sec. 1.823, the first sentence has been
modified by the deletion of the words ``in addition to and immediately
preceding.'' This change is consistent with WIPO Standard ST.25 (1998).
In paragraph (b) of Sec. 1.823, the fifth sentence has been
deleted, eliminating the prohibition of any item of information
occupying more than one line. This change is consistent with WIPO
Standard ST.25 (1998).
In paragraph (b) of Sec. 1.823, the last sentence has been deleted
to eliminate the ``rep'' designation for data elements of the
``Sequence Listing.'' Certain data elements may still be repeated
within the listing but this change was made for harmonization of the
table with WIPO Standard ST.25 (1998).
In paragraph (b) of Sec. 1.823, the eighth sentence has been
modified to reflect the new numeric numbering scheme, for harmonization
with WIPO Standard ST.25 (1998). Specifically, ``<100> through <193>''
of the proposed rule has been changed to ``<110> through <170>.''
The table in paragraph (b) of Sec. 1.823, has been changed to
reflect the revised numbering scheme and data elements used in WIPO
Standard ST.25 (1998). The specific changes are as follows:
Numeric identifier ``<100>, General Information,'' has been deleted
from the proposed rules, as it is not present in WIPO Standard ST.25
(1998).
Numeric identifier ``<110>, Applicant,'' in the proposed rule, has
been changed to indicate that ``preferably '' a maximum of ten names
may be indicated. This change allows for more than ten names in the
Applicant field for those instances in which such would be appropriate.
This change is consistent with WIPO Standard ST.25 (1998).
Numeric identifier ``<120>, Title of Invention,'' in the proposed
rule, has been changed to eliminate the limitation
[[Page 29631]]
that the title be a maximum of four lines. This change allows
applicants more flexibility with respect to the title. This change is
consistent with WIPO Standard ST.25 (1998).
Numeric identifier ``<130>, Number of Sequences,'' in the proposed
rule, has been changed to reflect ``<130>, File Reference,'' as stated
in WIPO Standard ST.25 (1998). This numeric identifier was indicated as
``<183>, File Reference/Docket Number '', in the rule as proposed. As
proposed this was an optional numeric identifier. The numeric
identifier remains optional once the application has been assigned an
application number, e.g., a serial number. This numeric identifier is
now MANDATORY when an application number has not yet been assigned to
the application, such as on the day the application is initially filed.
This change will assist in the matching of sequence information
submissions with an application in the event that either the paper copy
or the computer readable form were to become separated from the
remainder of the application. This change is consistent with WIPO
Standard ST.25 (1998).
The Number of Sequences field identified as ``<130>'' in the
proposed rule is now numbered ``<160>'' in Sec. 1.823 as adopted and
redefined as ``Number of SEQ ID NOs.''
The information associated with numeric identifiers ``<140>''
through ``<153>,'' ``Correspondence Address'' through ``Operating
System'' of the proposed rule, has been eliminated to reduce the burden
on the applicant and to harmonize with WIPO Standard ST.25 (1998). Some
of these numeric identifiers have been used in the new numbering scheme
and have been associated with different information as indicated herein
and in the Table of Sec. 1.823.
One remaining numeric identifier within the Computer Readable Form
section, ``<154>, Software,'' of the proposed rule, will remain, with
the exception that it has been reassigned the numeric identifier of
``<170>'' to reflect the numbering scheme presented in WIPO Standard
ST.25 (1998).
The main headings ``<160>, Current Application Data'' and ``<170>,
Prior Application Data,'' of the proposed rules, have been eliminated
to harmonize with WIPO Standard ST.25 (1998) and reduce the number of
fields in the Sequence Listing. The information that was to appear
under these main headings remains in the rules but has been reassigned
numeric identifiers <140> through <151>. The specific changes are as
follows: ``<160>'' has been redefined as ``Number of SEQ ID NOs '';
``<161>, Application Number,'' of the proposed rule is now numbered as
``<140>,'' and is defined as ``Current Application Number'; ``<162>,
Filing Date,'' of the proposed rule is now numbered ``<141>,'' and is
defined as ``Current Filing Date''; ``<170>'' has been redefined as
``Software ``; ``<171>, Application Number,'' of the proposed rule is
now numbered as ``<150>,'' and is defined as ``Prior Application
Number''; ``<172>, Filing Date,'' of the proposed rule is now numbered
as ``<151>,'' and is defined as ``Prior Application Filing Date.''
The numeric identifiers now numbered ``<150>, Prior Application
Number,'', and ``<151>, Prior Application Filing Date,'' are now
mandatory only in those instances in which a claim for priority with
respect to those prior applications is being made under either 35
U.S.C. 119 or 120. This change will provide information in this regard
when it is most useful and was necessary to harmonize these rules with
WIPO Standard ST.25 (1998). Throughout the Sequence Listing,
application numbers must be set forth as a combination of the two digit
country code, as set forth in WIPO Standard ST.3, as well as an
application number in accordance with WIPO Standard ST.13 or for an
international application, the numbering system as set out in Section
307(a) of the Administrative Instructions under the PCT.
Numeric identifiers ``<180>, Attorney/Agent Information,'' through
``<182>, Registration Number,'' of the proposed rule, have been
eliminated to harmonize with WIPO Standard ST.25 (1998) and reduce the
number of fields in the Sequence Listing.
Numeric identifier ``<183>, File Reference/Docket Number'' of the
proposed rule has been reassigned as numeric identifier ``<130>,'' and
redefined as ``File Reference'' in an effort to harmonize with WIPO
Standard ST.25 (1998).
The Telecommunication Information section, ``<190>'' through
``<193>'' of the proposed rules, has been eliminated in order to reduce
the number of fields in the Sequence Listing and harmonize with WIPO
Standard ST.25 (1998).
Numeric identifier ``<200>, Information for SEQ ID NO:#:'', has
been reassigned the numeric identifier ``<210>, SEQ ID NO: #:'' This
numeric identifier indicates the integer, referred to in these final
rules as the sequence identifier for both the sequence information and
the actual sequence which follows the information.
Numeric identifier ``<210>, Sequence Characteristics,'' of the
proposed rule has been eliminated in order to reduce the number of
required elements in the Sequence Listing and harmonize with WIPO
Standard ST.25 (1998).
The valid responses for the mandatory numeric identifier ``<212>,
Type,'' have been changed from ``N'' and ``A'', as stated in the
proposed rule, to ``DNA,'' ``RNA,'' and ``PRT'' (protein) in order to
harmonize with WIPO Standard ST.25 (1998). A compound that is a mixture
of DNA and RNA should be represented by ``DNA.'' This change is
consistent with WIPO Standard ST.25 (1998).
Numeric identifier ``<213>, Organism,'' has been added to the
Sequence Listing of these final rules in an effort to harmonize with
WIPO Standard ST.25 (1998). A response for the Organism identifier is
MANDATORY. The valid responses are the scientific name, i.e. ``Genus
species'', ``Artificial Sequence'', or ``Unknown.''
Numeric identifier ``<214>, Topology,'' of the proposed rule, has
been eliminated to harmonize with WIPO Standard ST.25 (1998), and to
reduce the burden on the applicant.
Numeric identifier ``<290>, Feature,'' has become numeric
identifier ``<220>, Feature.'' This numeric identifier has become
MANDATORY for those sequences in which numeric identifier ``<213>,
Organism,'' is completed with either ``Artificial Sequence'' or
``Unknown.'' This numeric identifier is also required if the compound
sequence is a mixture of DNA and RNA. Numeric identifier ``<220>,
Feature'' is a header only. No data are added immediately following
this numeric identifier. These changes are required to achieve
harmonization with WIPO Standard ST.25 (1998).
Numeric identifier ``<291>, Name/Key,'' has become numeric
identifier ``<221>, Name/Key.'' As proposed, the information provided
was restricted to a maximum of four lines. The four line restriction
has been removed to reduce the limitations on this field. The comment
section of this numeric identifier has been changed in that it now
indicates that the selection of a feature name or feature key is
preferably made from those listed in Tables 5 and 6 of WIPO Standard
ST.25 (1998). These tables are reproduced above and this preference for
the listed feature names and keys is consistent with the requirement of
WIPO Standard ST.25 (1998).
Numeric identifier ``<292>, Location,'' has become ``<222>,
Location,'' so as to be consistent with the numeric identifiers
contained in WIPO Standard ST.25 (1998).
[[Page 29632]]
Numeric identifier ``<294>, Other Information,'' has become numeric
identifier ``<223>, Other Information,'' so as to be consistent with
the numeric identifiers contained in WIPO Standard ST.25 (1998). This
numeric identifier has become MANDATORY for those sequences in which
numeric identifier ``<213>, Organism,'' is completed with either
``Artificial Sequence'' or ``Unknown''. Numeric identifier ``<223>,
Other Information,'' should contain source information in those
instances when the organism is unknown or is an artificial sequence.
For example, the source may be unknown because the material was
isolated from a mixed bacterial culture rather than a pure culture. In
such a case, numeric identifier ``<223>, Other Information,'' should be
completed by explaining the mixed culture source of the sequenced
material. If a sequence is completely synthesized this should be
indicated in numeric identifier ``<223>, Other Information,'' while
numeric identifier ``<213>, Organism,'' would indicate ``Artificial
Sequence.'' This change has been made to accomplish harmonization
between these rules and WIPO Standard ST.25 (1998) which contains the
same mandatory requirement in this regard.
Numeric identifiers ``<308>'' through ``<310>,'' referring to the
`` Patent Document Number,'' ``Filing Date'' and `` Publication Date,''
of the proposed rule, have been moved to numeric identifiers ``<310>''
to ``<312>,'' respectively, of this Final Rule in order to harmonize
with the numeric numbering scheme of WIPO Standard ST.25 (1998).
Citations in the Sequence Listing must comply with WIPO Standard ST.6
for publication numbers and WIPO Standard ST.16 for document codes.
New numeric identifiers ``<308>, Database Accession Number,'' and
``<309> Database Entry Date,'' have been added to the final rules to
harmonize with WIPO Standard ST.25 (1998). These fields were added to
the publication information section of WIPO Standard ST.25 (1998) to
give an applicant more opportunity to further identify a published
citation.
Numeric identifier <400> ``Sequence Description: SEQ ID NO:#:'' has
been changed to ``Sequence `` for clarity. Also for clarity, the
explanation in the table has been changed to ``SEQ ID NO shall follow
the numeric identifier and should appear on the line preceding the
sequence.''
The format of the date fields has been changed throughout the
Sequence Listing to accommodate for international conventions. All date
fields referenced in the Sequence Listing shall conform to WIPO
Standard ST.2. Because compliance with Secs. 1.821 through 1.825 as
amended should produce Sequence Listings that are acceptable to all
receiving offices, a standardized date field convention was required.
Section 1.824
In paragraph (a)(6) of Sec. 1.824, ``, the date on which the data
were recorded on the computer readable form'' was added after ``title
of the invention'' to harmonize with WIPO Standard ST.25 (1998)
requirements. While this requirement of Sec. 1.824 was proposed to be
eliminated, that proposal is not adopted for purposes of harmonization
with WIPO Standard ST.25 (1998). Also in paragraph (a)(6) of
Sec. 1.824, `` name and type of computer and'' was deleted to reduce
the requirements.
Section 1.825
In paragraphs (a), (b), and (d) of Sec. 1.825, the sentence ``Such
a statement must be a verified statement if made by a person not
registered to practice before the Office'' has been deleted. The
separate verification requirements in Sec. 1.825 have been eliminated
in view of the recent amendment to Secs. 1.4(d) and 10.18. See Changes
to Patent Practice and Procedure; Final Rule, 62 FR. 53131 (October 10,
1997), 1203 Off. Gaz. Pat. Office 63 (October 21, 1997).
Response to and Analysis of Comments
Six written comments were received in response to the Notice of
Proposed Rulemaking. Several of these comments address the three
specific queries set forth in the Notice of Proposed Rulemaking.
The first query posed in the Notice of Proposed Rulemaking was: (1)
Should the PTO accept voluntary submissions of computer readable forms
and Sequence Listings where a D-amino acid is contained in the
sequence? If such voluntary submissions are accepted, should there be a
restriction on the choice of identifying a D-amino acid by an Xaa or by
its L-amino acid counterpart abbreviation?
Comment: One comment indicated that not only should the PTO accept
voluntary submissions under these rules where a D-amino acid is
contained in the sequence, the Office should make such submissions
mandatory and designated by an Xaa. One comment indicated that
sequences containing D-amino acids should not be in the PTO databases.
Response: Upon careful consideration, the PTO has decided to accept
voluntary submissions of protein sequences containing D-amino acids.
The PTO strongly encourages anyone making such voluntary submissions to
identify a D-amino acid with an Xaa, describing the D-amino acid in the
Features section of the Sequence Listing. This section is indicated by
numeric identifiers <220> through <223> in 37 CFR 1.823. Procedural
concerns compel this acceptance of voluntary submissions. Computer
readable forms are processed prior to examination. It is cumbersome to
establish a viable procedure to redact any voluntary submissions out of
the PTO database. The use of Xaa to indicate a D-amino acid, should
such sequence information be submitted in accordance with these rules,
is encouraged so as to alert anyone reviewing the sequence that a
particular amino acid is other than a naturally occurring L-amino acid
and to more accurately depict the extent of similarities between such a
sequence and the L-amino acid containing sequences present in a
database being searched for examination or other purposes.
Because the sequence databases do not currently include D-amino
acids in sequences and thus are not searchable for such sequences, the
submission of those sequences containing D-amino acids will not be made
mandatory.
The second query posed in the proposed rules was: (2) Should the
provisions of 37 CFR 1.821(c) be altered to exclude some prior art
sequences from inclusion in the Sequence Listing even though they are
presented in a patent application disclosure as sequences? Should the
reference to an accession number of an admitted prior art sequence in a
publicly available, electronic, sequence database suffice and exclude
that sequence from the requirements of the sequence rules?
Comment: Four comments indicated that known ``prior art'' sequences
should not be required in the Sequence Listing. A referral to a
publicly available, electronic, sequence database for access to such
``prior art'' sequences would be an acceptable alternative to two of
those commenting on this aspect; the other two did not address this
point. The reasons given for excluding such sequences are the expense
and time required by applicants and their representatives in the
inclusion of ``prior art'' sequences that are considered to be ``non-
inventive''. Reducing the bulk of the paper copy of the Sequence
Listing was also mentioned.
Response: The requirement to submit all disclosed sequences in the
format required by Secs. 1.821 through 1.825 is
[[Page 29633]]
maintained. This point was discussed with officials from the JPO and
EPO. The offices have considered the stated concerns with regard to
costs to applicants. Sections 1.821 through 1.825 do not require any
information to be disclosed in the form of a sequence, but rather
require a particular format whenever information is presented in the
form of a sequence. Those applicants for whom compliance with the rules
remains a significant hardship may petition under Sec. 1.183 for a
waiver of the applicable requirement of Secs. 1.821 through 1.825.
The technical and legal concerns mentioned in the Notice of
Proposed Rulemaking still exist concerning the use of an alternative
reference to a publicly available, electronic, sequence database. These
concerns are: (1) What constitutes a publicly available, electronic,
sequence database? (2) Would the USPTO and the other patent offices
which have similar rules be required to produce a list of
internationally accepted databases? (3) What would be the criteria for
such acceptance? (4) An additional issue would exist involving
electronic records maintenance: is there any assurance that once
information is contained in a database that it will be retained and
available indefinitely without alteration? Changes to the information
in nucleic acid sequence databases resulting from the discovery of
sequencing errors are well-known.
(5) Does the mere existence of the sequence information in such a
record constitute reasonable means of retrieval? In other words, would
one need some text basis or other identifier to retrieve the
information?
Additional reasons for the inclusion of these prior art sequences
remain relevant. These reasons are: (1) the assessment of whether a
particular sequence falls within the requirements of the current rules
is simple; (2) the general public is assured that all patents which
contain any sequence information contain all of the sequence
information in the Sequence Listing and all sequences are available in
a computer accessible form; and (3) as a publication, the contextual
association of new and old information is potentially unique to the
patent and very valuable to anyone assessing the state of the art at
the time of a patented invention, and thus are desirable to be present
in electronic form in association with that patent.
The third query posed in the proposed rules was: (3) Should
Sequence Listings filed in an international application filed under the
PCT be published only electronically and made available for retrieval
electronically by an accession number from several sequence
repositories?
Comment: Two comments were received in response to this query, one
in favor and one opposed to limiting the publication of the Sequence
Listing to an electronic form for published PCT applications in the
international phase.
Response: At this time paper copies of the Sequence Listings filed
as part of the description will continue to be published in
applications filed under PCT. The PTO together with the EPO, JPO and
WIPO will continue to discuss the possibility of electronic
publication. However, any implementation of such electronic publication
in lieu of publication in paper form will not be undertaken until
further study has been completed.
Comment: One comment suggested that informative English words be
placed next to the numerical headings in the Sequence Listing as
printed in a U.S. patent.
Response: The PTO will provide English words corresponding to the
numeric identifiers in the printed U.S. patents.
Comment: One comment suggested addition of a descriptive comment
line to the Sequence Listing.
Response: The ``Other Information'' line in the Features section,
which is numeric identifier <223> in Sec. 1.823, provides for a
description of a sequence. While completion of this section is only
mandatory when the sequence contains ``n'', ``Xaa'', a modified or
unusual L-amino acid or a modified base, it is frequently completed in
other circumstances.
Comment: One comment requested we harmonize Secs. 1.821 through
1.825 with PCT, EPO and other authorities such that the differences in
the requirements for Sequence Listing submissions are minimal.
Response: This change to Secs. 1.821 through 1.825 is the result of
such an effort to harmonize the PTO, PCT, EPO and JPO Sequence Listing
requirements to the extent possible. The requirements of newly
developed WIPO ST.25 are substantially identical to the requirements of
amended Secs. 1.821 through 1.825. PatentIn Version 2.0 software, now
available, is drafted to meet all of the requirements of WIPO Standard
ST.25 (1998). The requirements of Secs. 1.821 through 1.825, however,
are less stringent than the requirements of WIPO Standard ST.25 (1998).
Thus, applicants who wish to file in countries which adhere to WIPO
Standard ST.25 (1998) should consider the following when not using
PatentIn Version 2.0:
1. The WIPO Standard ST.25 (1998) does not permit submissions using
a Macintosh computer.
2. The WIPO Standard ST.25 (1998) does not accept the range of
media permitted by amended Secs. 1.821 through 1.825.
3. The answers in field <221> and <222> must use selections from
Tables 5 and 6 of WIPO Standard ST.25 (1998) to comply with that
standard. The terms from these Tables are considered language neutral
vocabulary.
4. Any free text in numeric identifier <223> of a Sequence Listing
will not be translated and thus must also appear in the specification
of applications filed under WIPO Standard ST.25 (1998) for compliance.
5. A CRF filed after the filing of an application under the PCT
does not form part of the disclosure and will not be published in the
pamphlet.
6. Paragraph 39 of WIPO Standard ST.25 (1998) requires the specific
wording ``the information recorded on the form is identical to the
written sequence listing.''
7. WIPO Standard ST.25 (1998), paragraph 24, requires spaces
between specified numeric identifiers in the Sequence Listing.
Comment: One comment requested a WINDOWS based version
of PatentIn.
Response: A WINDOWS based version of PatentIn, PatentIn
2.0, has been developed through a Trilaterally-sponsored joint
initiative and is being made available.
Comment: One comment expressed concern over application of the
doctrine of equivalents by the courts to sequence-based claim language.
Response: Sections 1.821 through 1.825 do not establish a
disclosure requirement, nor do they alter the requirements of 35 U.S.C.
Sec. 112. They merely require a particular format whenever information
is presented in the form of a sequence. The use of sequence
identification numbers (SEQ ID NO: #) only provides a shorthand way for
applicants to refer to sequence information. These identification
numbers do not in any way restrict the manner in which an invention can
be claimed. Similarly, the use of this format does not impact the
potential interpretations and legal determinations that could be made
with respect to claims containing information in the form of a
nucleotide or amino acid sequence.
Comment: One comment requested the flexibility to use single-letter
amino acid codes.
Response: Sections 1.821 through 1.825 as amended do not constrain
an applicant from using single letter codes
[[Page 29634]]
in the disclosure. The requirements of the sequence searching and the
sequence storage mechanisms include only the three-letter codes, thus
the need for the constraint on the Sequence Listing information. There
is no such restriction on the sequence format in the body of the
disclosure or in the figures imposed by Secs. 1.821 through 1.825, or
any of the rules of practice; only the format for the Sequence Listing
is specified by Secs. 1.821 through 1.825.
Review Under the Paperwork Reduction Act of 1995
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 (PRA) unless that collection of information
displays a currently valid OMB control number.
This rule contains collections of information requirements subject
to the PRA. The principal impact of this Final Rule is: (1) Elimination
of certain requirements of Secs. 1.821 through 1.825; and (2) revision
of Secs. 1.821 through 1.825 for consistency with WIPO Standard ST.25
(1998), which will permit Sequence Listings to be presented in an
international, language neutral format.
The public reporting burden for these collections of information
have been approved by the Office of Management and Budget (OMB) under
OMB control number 0651-0024. The public reporting burden for this
collection of information is estimated to average 80 minutes per
response, including the time for reviewing instructions, searching
existing data sources, gathering and maintaining the information. Send
comments regarding this burden estimate or any other aspect of the data
requirements, including suggestions for reducing this burden, to Esther
M. Kepplinger at the address specified above or to the Office of
Information and Regulatory Affairs of OMB, New Executive Office Bldg.,
725 17th St. NW, rm. 10235, Washington, DC 20230, Attn: Desk Officer
for the Patent and Trademark Office.
Other Considerations
This Final Rule is in conformity with the requirements of the
Regulatory Flexibility Act (5 U.S.C. 601 et seq.), Executive Order
12612 (October 26, 1987), and the Paperwork Reduction Act of 1995 (44
U.S.C. 3501 et seq.). It has been determined that this rulemaking is
not significant for the purposes of Executive Order 12866 (September
30, 1993).
The Assistant General Counsel for Legislation and Regulation of the
Department of Commerce has certified to the Chief Counsel for Advocacy,
Small Business Administration that this Final Rule would not have a
significant impact on a substantial number of small entities
(Regulatory Flexibility Act, 5 U.S.C. 605(b)). The principal impact of
this Final Rule is: (1) Elimination of certain requirements of
Secs. 1.821 through 1.825; and (2) revision of Secs. 1.821 through
1.825 for consistency with WIPO Standard ST.25 (1998), which will
permit Sequence Listings to be presented in an international, language
neutral format.
The Office has determined that this Final Rule has no Federalism
implications affecting the relationship between the National Government
and the States as outlined in Executive Order 12612.
List of Subjects in 37 CFR Part 1
Administrative practice and procedure, Courts, Freedom of
information, Inventions and patents, Incorporation by reference,
Reporting and recordkeeping requirements, Small businesses.
For the reasons set forth in the preamble and under the authority
granted to the Commissioner of Patents and Trademarks by 35 U.S.C. 6,
Title 37 of the Code of Federal Regulations, part 1, is amended as
follows:
PART 1--RULES OF PRACTICE IN PATENT CASES
1. The authority citation for 37 CFR part 1 continues to read as
follows:
Authority: 35 U.S.C. 6, unless otherwise noted.
2. Section 1.821 is revised 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 Secs. 1.821
through 1.825 are interpreted to mean an unbranched sequence of four or
more amino acids or an unbranched sequence of ten 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 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 (1998), including Tables 1 through 6 in Appendix 2,
herein incorporated by reference. (Hereinafter ``WIPO Standard ST.25
(1998)''). This incorporation by reference was approved by the Director
of the Federal Register in accordance with 5 U.S.C. 552(a) and 1 CFR
part 51. Copies of WIPO Standard ST.25 (1998) may be obtained from the
World Intellectual Property Organization; 34 chemin des Colombettes;
1211 Geneva 20 Switzerland. Copies of ST.25 may be inspected at the
Patent Search Room; Crystal Plaza 3, Lobby Level; 2021 South Clark
Place; Arlington, VA 22202. Copies may also be inspected at the Office
of the Federal Register, 800 North Capitol Street, NW, Suite 700,
Washington, DC. 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 WIPO
Standard ST.25 (1998), Appendix 2, Table 1. Modifications, e.g.,
methylated bases, may be described as set forth in WIPO Standard ST.25
(1998), Appendix 2, Table 2, 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 WIPO Standard ST.25
(1998), Appendix 2, Table 3. 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 WIPO Standard ST.25 (1998),
Appendix 2, Table 3 with the modified positions; e.g., hydroxylations
or glycosylations, being described as set forth in WIPO Standard ST.25
(1998), Appendix 2, Table 4, 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 WIPO Standard ST.25
(1998), Appendix 2, Table 3 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.
(b) Patent applications which contain disclosures of nucleotide
and/or amino acid sequences, in accordance with the definition in
paragraph (a) of this section, shall, with regard to the manner in
which the nucleotide and/or amino
[[Page 29635]]
acid sequences are presented and described, conform exclusively to the
requirements of Secs. 1.821 through 1.825.
(c) Patent applications which contain disclosures of nucleotide
and/or amino acid sequences must contain, as a separate part of the
disclosure, a paper copy disclosing the nucleotide and/or amino acid
sequences and associated information using the symbols and format in
accordance with the requirements of Secs. 1.822 and 1.823. This paper
copy is hereinafter referred to as the ``Sequence Listing.'' Each
sequence disclosed must appear separately in the ``Sequence Listing.''
Each sequence set forth in the ``Sequence Listing'' shall be assigned a
separate sequence identifier. The sequence identifiers shall begin with
1 and increase sequentially by integers. If no sequence is present for
a sequence identifier, the code ``000'' shall be used in place of the
sequence. The response for the numeric identifier <160> shall include
the total number of SEQ ID NOs, whether followed by a sequence or by
the code ``000.''
(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 the sequence identifier, 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.
(e) A copy of the ``Sequence Listing'' referred to in paragraph (c)
of this section must also be submitted in computer readable form in
accordance with the requirements of Sec. 1.824. The computer readable
form is a copy of the ``Sequence Listing'' and will not necessarily be
retained as a part of the patent application file. If the computer
readable form of a new application is to be identical with the computer
readable form of another application of the applicant on file in the
Patent and Trademark Office, reference may be made to the other
application and computer readable form in lieu of filing a duplicate
computer readable form in the new application if the computer readable
form in the other application was compliant with all of the
requirements of these rules. The new application shall be accompanied
by a letter making such reference to the other application and computer
readable form, both of which shall be completely identified. In the new
application, applicant must also request the use of the compliant
computer readable ``Sequence Listing'' that is already on file for the
other application and must state that the paper copy of the ``Sequence
Listing'' in the new application is identical to the computer readable
copy filed for the other application.
(f) In addition to the paper copy required by paragraph (c) of this
section and the computer readable form required by paragraph (e) of
this section, a statement that the content of the paper and computer
readable copies are the same must be submitted with the computer
readable form, e.g., a statement that ``the information recorded in
computer readable form is identical to the written sequence listing.''
(g) If any of the requirements of paragraphs (b) through (f) 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, 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 submission in reply to a requirement under this
paragraph must be accompanied by a statement that the submission
includes no new matter.
(h) If any of the requirements of paragraphs (b) through (f) of
this section are not satisfied at the time of filing an international
application under the Patent Cooperation Treaty (PCT), which
application is to be searched by the United States International
Searching Authority or examined by the United States International
Preliminary Examining Authority, applicant will be sent a notice
necessitating compliance with the requirements within a prescribed time
period. Any submission in reply to a requirement under this paragraph
must be accompanied by a statement that the submission does not include
matter which goes beyond the disclosure in the international
application as filed. If applicant fails to timely provide the required
computer readable form, the United States International Searching
Authority shall search only to the extent that a meaningful search can
be performed without the computer readable form and the United States
International Preliminary Examining Authority shall examine only to the
extent that a meaningful examination can be performed without the
computer readable form.
3. Section 1.822 is revised to read as follows:
Sec. 1.822 Symbols and format to be used for nucleotide and/or amino
acid sequence data.
(a) The symbols and format to be used for nucleotide and/or amino
acid sequence data shall conform to the requirements of paragraphs (b)
through (e) of this section.
(b) The code for representing the nucleotide and/or amino acid
sequence characters shall conform to the code set forth in the tables
in WIPO Standard ST.25 (1998), Appendix 2, Tables 1 and 3. This
incorporation by reference was approved by the Director of the Federal
Register in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies
of ST.25 may be obtained from the World Intellectual Property
Organization; 34 chemin des Colombettes; 1211 Geneva 20 Switzerland.
Copies of ST.25 may be inspected at the Patent Search Room; Crystal
Plaza 3, Lobby Level; 2021 South Clark Place; Arlington, VA 22202.
Copies may also be inspected at the Office of the Federal Register, 800
North Capitol Street, NW, Suite 700, Washington, DC. 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 WIPO Standard ST.25 (1998), Appendix 2, Tables 2
and 4, and the modification is also set forth in the Feature section.
Otherwise, each occurrence of a base or amino acid not appearing in
WIPO Standard ST.25 (1998), Appendix 2, Tables 1 and 3, shall be listed
in a given sequence as ``n'' or ``Xaa,'' respectively, with further
information, as appropriate, given in the Feature section, preferably
by including one or more feature keys listed in WIPO Standard ST.25
(1998), Appendix 2, Tables 5 and 6.
(c) Format representation of nucleotides. (1) A nucleotide sequence
shall be listed using the lower-case letter for representing the one-
letter code for the nucleotide bases set forth in WIPO Standard ST.25
(1998), Appendix 2, Table 1.
(2) The bases in a nucleotide sequence (including introns) shall be
listed in groups of 10 bases except in the coding parts of the
sequence. Leftover bases, fewer than 10 in number, at the end of
noncoding parts of a sequence shall be grouped together and separated
from adjacent groups of 10 or 3 bases by a space.
(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 typed
immediately below the corresponding codons. Where a codon spans an
intron, the amino acid symbol
[[Page 29636]]
shall be typed below the portion of the codon containing two
nucleotides.
(4) A nucleotide sequence shall be listed with a maximum of 16
codons or 60 bases per line, with a space provided between each codon
or group of 10 bases.
(5) A nucleotide sequence shall be presented, 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 be marked 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.
(7) For those nucleotide sequences that are circular in
configuration, the enumeration method set forth in paragraph (c)(6) of
this section remains applicable with the exception that the designation
of the first base of the nucleotide sequence may be made at the option
of the applicant.
(d) Representation of amino acids. (1) The amino acids in a protein
or peptide sequence shall be listed using the three-letter abbreviation
with the first letter as an upper case character, as in WIPO Standard
ST.25 (1998), Appendix 2, Table 3.
(2) A protein or peptide sequence shall be listed with a maximum of
16 amino acids per line, with a space provided between each amino acid.
(3) An amino acid sequence shall be presented in the amino to
carboxy direction, from left to right, and the amino and carboxy groups
shall not be presented 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 presented,
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. It shall be marked below
the sequence every 5 amino acids. 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 represented
as a single amino acid sequence, but shall be presented as separate
amino acid sequences.
(e) A sequence with a gap or gaps shall be presented as a plurality
of separate sequences, with separate sequence identifiers, with the
number of separate sequences being equal in number to the number of
continuous strings of sequence data. A sequence that is made up of one
or more noncontiguous segments of a larger sequence or segments from
different sequences shall be presented as a separate sequence.
4. Section 1.823 is revised to read as follows:
Sec. 1.823 Requirements for nucleotide and/or amino acid sequences as
part of the application papers.
(a) The ``Sequence Listing'' required by Sec. 1.821(c), setting
forth the nucleotide and/or amino acid sequences and associated
information in accordance with paragraph (b) of this section, must
begin on a new page and must be titled ``Sequence Listing''. The
``Sequence Listing'' preferably should be numbered independently of the
numbering of the remainder of the application. Each page of the
``Sequence Listing'' should contain no more than 66 lines and each line
should contain no more than 72 characters. A fixed-width font should be
used exclusively throughout the ``Sequence Listing.''
(b) The ``Sequence Listing'' shall, except as otherwise indicated,
include the actual nucleotide and/or amino acid sequence, the numeric
identifiers and their accompanying information as shown in the
following table. The numeric identifier shall be used only in the
``Sequence Listing.'' The order and presentation of the items of
information in the ``Sequence Listing'' shall conform to the
arrangement given below. Each item of information shall begin on a new
line and shall begin with the numeric identifier enclosed in angle
brackets as shown. 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. Numeric identifiers
<110> through <170> shall only be set forth at the beginning of the
``Sequence Listing.'' The following table illustrates the numeric
identifiers.
----------------------------------------------------------------------------------------------------------------
Mandatory (M) or optional
Numeric identifier Definition Comments and format (O).
----------------------------------------------------------------------------------------------------------------
<110>.................... Applicant............... Preferably max. of 10 names; M.
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 of appl. number.
<140>.................... Current Application Specify as: US 07/999,999 or M, if available.
Number. PCT/US96/99999.
<141>.................... Current Filing Date..... Specify as: yyyy-mm-dd....... M, if available.
<150>.................... Prior Application Number Specify as: US 07/999,999 or M, if applicable include
PCT/US96/99999. priority documents under 35
USC 119 and 120.
<151>.................... Prior Application Filing Specify as: yyyy-mm-dd....... M, if applicable.
Date.
<160>.................... Number of SEQ ID NOs.... Count includes total number M.
of SEQ ID NOs.
<170>.................... Software................ Name of software used to O.
create the Sequence Listing.
<210>.................... SEQ ID NO:#:............ Response shall be an integer M.
representing the SEQ ID NO
shown.
<211>.................... Length.................. Respond with an integer M.
expressing the number of
bases or amino acid residues.
[[Page 29637]]
<212>.................... Type.................... Whether presented sequence M.
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. Genus/ M
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 <220>. <221- m,="" under="" the="" following="" 223=""> provide for a conditions: if ``n,''
description of points of ``Xaa,'' or a modified or
biological significance in unusual L-amino acid or
the sequence.. modified base was used in a
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 feature, conditions: if ``n,''
preferably from WIPO ``Xaa,'' or a modified or
Standard ST.25 (1998), unusual L-amino acid or
Appendix 2, Tables 5 and 6. modified base was used in a
sequence.
<222>.................... Location................ Specify location within M, under the following
sequence; where appropriate conditions: if ``n,''
state number of first and ``Xaa,'' or a modified or
last bases/amino acids in unusual L-amino acid or
feature. modified base was used in a
sequence.
<223>.................... Other Information....... Other relevant information; M, under the following
four lines maximum. conditions: if ``n,''
``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 ten named O.
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 data O.
published; specify as yyyy-
mm-dd, MMM-yyyy or Season-
yyyy.
<308>.................... Database Accession Accession number assigned by O.
Number. database including database
name.
<309>.................... Database Entry Date..... Date of entry in database; O.
specify as yyyy-mm-dd or MMM-
yyyy.
<310>.................... Patent Document Number.. Document number; for patent- O.
type citations only. Specify
as, for example, US 07/
999,999.
<311>.................... Patent Filing Date...... Document filing date, for O.
patent-type citations only;
specify as yyyy-mm-dd.
<312>.................... Publication Date........ Document publication date, O.
for patent-type citations
only; specify as yyyy-mm-dd.
<313>.................... Relevant Residues....... FROM (position) TO (position) O.
<400>.................... Sequence................ SEQ ID NO should follow the M.
numeric identifier and
should appear on the line
preceding the actual
sequence.
----------------------------------------------------------------------------------------------------------------
5. Section 1.824 is revised to read as follows:
Sec. 1.824 Form and format for nucleotide and/or amino acid sequence
submissions in computer readable form.
(a) The computer readable form required by Sec. 1.821(e) shall meet
the following specifications:
(1) The computer readable form shall contain a single ``Sequence
Listing'' as either a diskette, series of diskettes, or other
permissible media outlined in paragraph (c) of this section.
(2) The ``Sequence Listing'' in paragraph (a) (l) of this section
shall be submitted in American Standard Code for Information
Interchange (ASCII) text. No other formats shall be allowed.
(3) The computer readable form may be created by any means, such as
word processors, nucleotide/amino acid sequence editors or other custom
computer programs; however, it shall conform to all specifications
detailed in this section.
(4) File compression is acceptable when using diskette media, so
long as the compressed file is in a self-extracting format that will
decompress on one of the systems described in paragraph (b) of this
section.
(5) Page numbering shall not appear within the computer readable
form version of the ``Sequence Listing'' file.
(6) All computer readable forms shall have a label permanently
affixed thereto on which has been hand-printed or typed: the name of
the applicant, the title of the invention, the date on which the data
were recorded on the computer readable form, the operating system used,
a reference number, and an application serial number and filing date,
if known.
[[Page 29638]]
(b) Computer readable form submissions must meet these format
requirements:
(1) Computer: IBM PC/XT/AT, or compatibles, or Apple Macintosh;
(2) Operating System: MS-DOS, Unix or Macintosh;
(3) Line Terminator: ASCII Carriage Return plus ASCII Line Feed;
(4) Pagination: Continuous file (no ``hard page break'' codes
permitted);
(c) Computer readable form files submitted may be in any of the
following media:
(1) Diskette : 3.50 inch, 1.44 Mb storage; 3.50 inch, 720 Kb
storage; 5.25 inch, 1.2 Mb storage; 5.25 inch, 360 Kb storage.
(2) Magnetic tape: 0.5 inch, up to 24000 feet; Density: 1600 or
6250 bits per inch, 9 track; Format: Unix tar command; specify blocking
factor (not ``block size''); Line Terminator: ASCII Carriage Return
plus ASCII Line Feed.
(3) 8mm Data Cartridge: Format: Unix tar command; specify blocking
factor (not ``block size''); Line Terminator: ASCII Carriage Return
plus ASCII Line Feed.
(4) CD-ROM: Format: ISO 9660 or High Sierra Format
(5) Magneto Optical Disk: Size/Storage Specifications: 5.25 inch,
640 Mb.
(d) Computer readable forms that are submitted to the Office will
not be returned to the applicant.
6. Section 1.825 is revised to read as follows:
Sec. 1.825 Amendments to or replacement of sequence listing and
computer readable copy thereof.
(a) Any amendment to the paper copy of the ``Sequence Listing''
(Sec. 1.821(c)) must be made by the submission of substitute sheets.
Amendments must be accompanied by a statement that indicates support
for the amendment in the application, as filed, and a statement that
the substitute sheets include no new matter.
(b) Any amendment to the paper copy of the ``Sequence Listing,'' in
accordance with paragraph (a) of this section, must be accompanied by a
substitute copy of the computer readable form (Sec. 1.821(e)) including
all previously submitted data with the amendment incorporated therein,
accompanied by a statement that the copy in computer readable form is
the same as the substitute copy of the ``Sequence Listing.''
(c) Any appropriate amendments to the ``Sequence Listing'' in a
patent; e.g., by reason of reissue or certificate of correction, must
comply with the requirements of paragraphs (a) and (b) of this section.
(d) If, upon receipt, the computer readable form is found to be
damaged or unreadable, applicant must provide, within such time as set
by the Commissioner, a substitute copy of the data in computer readable
form accompanied by a statement that the substitute data is identical
to that originally filed.
7. Appendix A To Subpart G to Part 1 is revised to read as follows:
BILLING CODE 3510-16-P
[[Page 29639]]
Appendix A To Subpart G to Part 1--Sample Sequence Listing
[GRAPHIC] [TIFF OMITTED] TR01JN98.006
[[Page 29640]]
[GRAPHIC] [TIFF OMITTED] TR01JN98.007
[[Page 29641]]
[GRAPHIC] [TIFF OMITTED] TR01JN98.008
[[Page 29642]]
[GRAPHIC] [TIFF OMITTED] TR01JN98.009
[[Page 29643]]
[GRAPHIC] [TIFF OMITTED] TR01JN98.010
Dated: May 22, 1998.
Bruce A. Lehman,
Assistant Secretary of Commerce and Commissioner of Patents and
Trademarks.
[FR Doc. 98-14194 Filed 5-29-98; 8:45 am]
BILLING CODE 3510-16-C
