2412.02(a) “Enumeration of its residues” [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b).]

WIPO Standard ST.26 specifies that “enumeration of its residues” means “disclosure of a sequence in a patent application by listing, in order, each residue of the sequence, wherein either (i) the residue is represented by a name, abbreviation, symbol, or structure (e.g., HHHHHHQ or HisHisHisHisHisHisGln); or (ii) multiple residues are represented by a shorthand formula (e.g., His6Gln) (WIPO Standard ST.26, paragraph 3(c)). See also the Guidance portion of the Standard, Annex VI, page 3.26.vi.2 for a discussion of “enumeration of its residues” and page 3.26.vi.18-19, 51, 53 for examples.

2412.03(a) “Specifically Defined” [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b).]

WIPO Standard ST.26, paragraph 3(k), provides that “specifically defined” means any nucleotide other than those represented by the symbol “n” and any amino acid other than those represented by the symbol “X,”, wherein “n” and “X” are used in a conventional manner as shown below in Table 1 for nucleotide symbols and Table 3 for amino acids symbols.

Table 1: List of Nucleotides Symbols

Symbol	Definition
a	adenine
c	cytosine
g	guanine
t	thymine in DNA/uracil in RNA (t/u)
m	a or c
r	a or g
w	a or t/u
s	c or g
y	c or t/u
k	g or t/u
v	a or c or g; not t/u
h	a or c or t/u; not g
d	a or g or t/u; not c
b	c or g or t/u; not a
n	a or c or g or t/u; “unknown” or “other”

Reproduced from WIPO Standard ST.26, Annex I, Section 1.

Table 3: List of Amino Acids Symbols

Symbol	Definition
A	Alanine
R	Arginine
N	Asparagine
D	Aspartic acid (Aspartate)
C	Cysteine
Q	Glutamine
E	Glutamic acid (Glutamate)
G	Glycine
H	Histidine
I	Isoleucine
L	Leucine
K	Lysine
M	Methionine
F	Phenylalanine
P	Proline
O	Pyrrolysine
S	Serine
U	Selenocysteine
T	Threonine
W	Tryptophan
Y	Tyrosine
V	Valine
B	Aspartic acid or Asparagine
Z	Glutamine or Glutamic acid
J	Leucine or Isoleucine
X	A or R or N or D or C or Q or E or G or H or I or L or K or M or F or P or O or S or U or T or W or Y or V; “unknown” or “other”

Reproduced from WIPO Standard ST.26, Annex I, Section 3.

2412.03(b) “Amino Acid” [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). ]

WIPO Standard ST.26, paragraph 3(a), defines “amino acid” to mean any amino acid that can be represented using any of the symbols shown in Annex I, Table 3: List of Amino Acids Symbols of WIPO Standard ST.26 (reproduced in MPEP § 2412.03(a)). Such amino acids include, inter alia, D-amino acids and amino acids containing modified or synthetic side chains. Amino acids will be construed as unmodified L-amino acids unless further described in a “feature table”. See MPEP § 2413.01(g), subsection I, for discussion of a “feature table”. A peptide nucleic acid (PNA) residue is not considered an amino acid, but is considered a nucleotide.

2412.03(c) “Modified Amino Acid” [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/ standards/en/pdf/03-26-01.pdf.]

WIPO Standard ST.26, paragraph 3(e), defines “modified amino acid” to mean any amino acid as described in the definition of “amino acid”, other than L-alanine, L-arginine, L-asparagine, L-aspartic acid, L-cysteine, L-glutamine, L-glutamic acid, L-glycine, L-histidine, L-isoleucine, L-leucine, L-lysine, L-methionine, L-phenylalanine, L-proline, L-pyrrolysine, L-serine, L-selenocysteine, L-threonine, L-tryptophan, L-tyrosine, or L-valine. See MPEP § 2412.03(b).

Modified amino acids, including D-amino acids, should be represented in the sequence as the corresponding unmodified amino acids whenever possible. Any modified amino acid in a sequence that cannot otherwise be represented by a symbol set forth in Table 3 must be represented by “X”, i.e., an “other” amino acid.

A modified amino acid must be further described in a feature table. See MPEP § 2413.01(g), subsection I, for discussion of a “feature table”. Where applicable, the feature keys “CARBOHYD” or “LIPID” should be used together with the qualifier “note”. The feature key “MOD_RES” should be used for other post-translationally modified amino acids together with the qualifier “note”. The feature key “SITE” together with the qualifier “note” should be used when the modified amino acid is not a post-translationally modified amino acid. See MPEP § 2413.01(g), subsections II and III, for discussion of a “feature key”. The value for the qualifier “note” must either be an abbreviation set forth in Table 4 below or the complete, unabbreviated name of the modified amino acid. The abbreviations set forth in Table 4 or the complete, unabbreviated names must not be used in the sequence itself.

Table 4: List of Modified Amino Acids

Abbreviation	Modified Amino acid
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
alle	allo-Isoleucine
MeGly	N-Methylglycine, sarcosine
Melle	N-Methylisoleucine
MeLys	6-N-Methyllysine
MeVal	N-Methylvaline
Nva	Norvaline
Nle	Norleucine
Orn	Ornithine

Reproduced from WIPO Standard ST.26, Annex I, Section 4.

2412.03(d) “Nucleotide” [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/ standards/en/pdf/03-26-01.pdf.]

WIPO Standard ST.26, paragraphs 3(f) and (g), identify a “nucleotide” to encompass any nucleotide or nucleotide analogue or “modified nucleotide” (see MPEP § 2412.03(e)) that can be represented using any of the symbols set forth in Table 1: List of Nucleotides Symbols (see MPEP § 2412.03(a)), wherein the nucleotide, or nucleotide analogue, or modified nucleotide contains:

• (i) a backbone moiety selected from:
  • (1) 2’ deoxyribose 5’ monophosphate (the backbone moiety of a deoxyribonucleotide) or ribose 5’ monophosphate (the backbone moiety of a ribonucleotide); or
  • (2) an analogue of a 2’ deoxyribose 5’ monophosphate or ribose 5’ monophosphate, which when forming the backbone of a nucleic acid analogue, results in an arrangement of nucleobases that mimics the arrangement of nucleobases in nucleic acids containing a 2’ deoxyribose 5’ monophosphate or ribose 5’ monophosphate backbone, wherein the nucleic acid analogue is capable of base pairing with a complementary nucleic acid; examples of backbone moieties include amino acids as in peptide nucleic acids, glycol molecules as in glycol nucleic acids, threofuranosyl sugar molecules as in threose nucleic acids, morpholine rings and phosphorodiamidate groups as in morpholinos, and cyclohexenyl molecules as in cyclohexenyl nucleic acids; and
• (ii) the backbone moiety is either:
  • (1) joined to a nucleobase, including a modified or synthetic purine or pyrimidine nucleobase; or
  • (2) lacking a purine or pyrimidine nucleobase when the nucleotide is part of a nucleotide sequence, referred to as an “AP site” or an “abasic site”.

2412.03(e) “Modified Nucleotide” [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/ standards/en/pdf/03-26-01.pdf.]

WIPO Standard ST.26, paragraph 3(f), provides that a “modified nucleotide” means any “nucleotide” as explained in MPEP § 2412.03(d) other than deoxyadenosine 3’-monophosphate, deoxyguanosine 3’-monophosphate, deoxycytidine 3’-monophosphate, deoxythymidine 3’-monophosphate, adenosine 3’-monophosphate, guanosine 3’-monophosphate, cytidine 3’-monophosphate, or uridine 3’-monophosphate.

2412.05(a) Use of Sequentially Numbered Sequence Identifiers in the “Sequence Listing XML” [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/standards/en/pdf/03-26-01.pdf.]

In accordance with 37 CFR 1.832(a), the sequence identifiers in the “Sequence Listing XML” must begin with 1 and increase sequentially by integers. The requirement for sequence identifiers, at a minimum, requires that each sequence be assigned a different number for purposes of identification. However, where practical and for ease of reference, sequences should be presented in the “Sequence Listing XML” in numerical order and in the order in which they are discussed in the application.

Each nucleotide and/or amino acid sequence that meets the definition in 37 CFR 1.831(b) and is enumerated by its residues must be assigned a separate sequence identifier, including a sequence which is identical to a region of a longer sequence. See MPEP § 2412.02 for further description of a “sequence”.

Where no sequence is present for a sequence identifier, i.e. an intentionally skipped sequence, “000” must be used in place of a sequence in a “Sequence Listing XML”. The total number of sequences indicated in the “Sequence Listing XML” must equal the total number of sequence identifiers, whether followed by a sequence or by “000”.

WIPO Standard ST.26 paragraphs 58 and 59 require that an intentionally skipped sequences in a “Sequence Listing XML” must be represented as follows:

• (a) the value of the element SequenceData and its attribute sequenceIDNumber, is the sequence identifier of the skipped sequence;
• (b) no value is provided for the elements INSDSeq _length, INSDSeq _moltype, and INSDSeq _division;
• (c) the element INSDSeq _feature-table is not included; and
• (d) the value of the element INSDSeq _sequence is the string “000”.

2412.05(b) Representation and Symbols of Nucleotide Sequence Data [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/standards/en/pdf/03-26-01.pdf.]

I. REPRESENTATION OF NUCLEOTIDE SEQUENCE

WIPO Standard ST.26, paragraph 11, provides that a nucleotide sequence must be represented only by a single strand, in the 5’ to 3’ direction from left to right, or in the direction from left to right that mimics the 5’ to 3’ direction. The designations 5’ and 3’ or any other similar designations must not be included in the sequence. A double-stranded nucleotide sequence disclosed by enumeration of the residues of both strands must be represented as:

• (a) a single sequence or as two separate sequences, each assigned its own sequence identifier, where the two separate strands are fully complementary to each other, or
• (b) two separate sequences, each assigned its own sequence identifier, where the two strands are not fully complementary to each other.

WIPO Standard ST.26, paragraph 12, provides that the first nucleotide presented in the sequence is residue position number 1. When nucleotide sequences are circular in configuration, applicant must choose the nucleotide in residue position number 1. Numbering is continuous throughout the entire sequence in the 5’ to 3’ direction, or in the direction that mimics the 5’ to 3’ direction. The last residue position number must equal the number of nucleotides in the sequence.

II. SYMBOLS FOR A NUCLEOTIDE SEQUENCE

WIPO Standard ST.26, paragraph 13, provides that all nucleotides in a sequence must be represented using the symbols as listed in Table 1: List of Nucleotides Symbols (see MPEP § 2412.03(a)). Only lower-case letters must be used. Any symbol used to represent a nucleotide is the equivalent of only one residue.

WIPO Standard ST.26, paragraph 14, sets forth that the symbol “t” will be construed as thymine in deoxyribonucleic acid (DNA) and uracil in ribonucleic acid (RNA). Uracil in DNA or thymine in RNA is considered a modified nucleotide and must be further described in a feature table. See MPEP § 2413.01(g), subsection I for more detail regarding a “feature table.”

WIPO Standard ST.26, paragraph 15, provides that where an ambiguity symbol (representing two or more alternative nucleotides) is appropriate, the most restrictive symbol should be used, as listed in Table 1: List of Nucleotides Symbols (see MPEP § 2412.03(a)). For example, if a nucleotide in a given position could be “a” or “g”, then “r” should be used, rather than “n”. The symbol “n” will be construed as any one of “a”, “c”, “g”, or “t/u” except where it is used with a further description in a feature table. The symbol “n” must not be used to represent anything other than a nucleotide. A single modified or “unknown” nucleotide may be represented by the symbol “n”, together with a further description in a feature table. See MPEP § 2413.01(g), subsection I, for more detail regarding a “feature table.” For representation of sequence variants, i.e., alternatives, deletions, insertions or substitutions relative to a primary sequence, see MPEP § 2412.05(c); and also MPEP § 2413.01(g), subsection XII for information on variants.

WIPO Standard ST.26, paragraph 16, sets forth that modified nucleotides should be represented in the sequence as the corresponding unmodified nucleotides, i.e., “a”, “c”, “g” or “t” whenever possible. Any modified nucleotide in a sequence that cannot otherwise be represented by any other symbol in Table 1: List of Nucleotides Symbols (see MPEP § 2412.03(a)), i.e., an “other” nucleotide, such as a non-naturally occurring nucleotide, must be represented by the symbol “n”. The symbol “n” is the equivalent of only one residue.

WIPO Standard ST.26, paragraph 19, specifies that uracil in DNA or thymine in RNA are considered modified nucleotides and must be represented in the sequence as “t” and be further described in a feature table using the feature key “modified_base”, the qualifier “mod_base” with “OTHER” as the qualifier value and the qualifier “note” with “uracil” or “thymine”, respectively, as the qualifier value. See MPEP § 2413.01(g), subsection I for more detail regarding a “feature table.”

WIPO Standard ST.26, paragraph 21, provides that any “unknown” nucleotide must be represented by the symbol “n” in the sequence. An “unknown” nucleotide should be further described in a feature table using the feature key “unsure”. The symbol “n” is the equivalent of only one residue. See MPEP § 2413.01(g), subsection I, for more detail regarding a “feature table.”

III. DESCRIPTION OF MODIFIED NUCLEOTIDES WITHIN A NUCLEOTIDE SEQUENCE

WIPO Standard ST.26, paragraph 17, specifies that a modified nucleotide must be further described in a feature table (see MPEP § 2413.01(g), subsection I, for more detail regarding a “feature table”) using the feature key “modified_base” and the mandatory qualifier “mod_base” in conjunction with a single abbreviation from Table 2: List of Modified Nucleotides, below, as the qualifier value. See MPEP § 2413.01(g) subsections II and III, for more information regarding use of a feature key; and MPEP § 2413.01(g) subsections V and VI, for more information regarding use of a qualifier. If the abbreviation is “OTHER”, the complete unabbreviated name of the modified nucleotide must be provided as the value in a “note” qualifier. For a listing of alternative modified nucleotides, the qualifier value “OTHER” may be used in conjunction with a further “note” qualifier. The abbreviations (or full names) provided in Table 2 must not be used in the sequence itself.

WIPO Standard ST.26, paragraph 18, describes that a nucleotide sequence including one or more regions of consecutive modified nucleotides that share the same backbone moiety must be further described in a feature table as required for a modified nucleotide. See MPEP § 2413.01(g), subsection I, for information regarding a feature table and MPEP § 2412.03(e) regarding modified nucleotides. The modified nucleotides of each such region may be jointly described in a single INSDFeature element of a “feature table” as described below. See MPEP § 2413.01(g), subsection I, for information regarding INSDFeature elements of a feature table. The most restrictive unabbreviated chemical name that encompasses all of the modified nucleotides in the range or a list of the chemical names of all the nucleotides in the range must be provided as the value in the “note” qualifier. For example, a glycol nucleic acid sequence containing “a”, “c”, “g”, or “t” nucleobases may be described in the “note” qualifier as “2,3-dihydroxypropyl nucleosides.” Alternatively, the same sequence may be described in the “note” qualifier as “2,3-dihydroxypropyladenine, 2,3-dihydroxypropylthymine, 2,3-dihydroxypropylguanine, or 2,3-dihydroxypropylcytosine.” Where an individual modified nucleotide in the region includes an additional modification, then the modified nucleotide must also be further described in the feature table as required for a modified nucleotide.

WIPO Standard ST.26, paragraph 19, provides that uracil in DNA or thymine in RNA are considered modified nucleotides and must be represented in the sequence as “t” and be further described in a feature table using the feature key “modified_base”, the qualifier “mod_base” with “OTHER” as the qualifier value and the qualifier “note” with “uracil” or “thymine”, respectively, as the qualifier value.See MPEP § 2413.01(g), subsections II and III, for more information regarding use of a feature key; and MPEP § 2413.01(g), subsections V and VI, for more information regarding use of a qualifier.

Table 2: List of Modified Nucleotides

Abbreviation	Definition
ac4c	4-acetylcytidine
chm5u	5-(carboxyhydroxymethyl)uridine
cm	2'-O-methylcytidine
cmnm5s2u	5-carboxymethylaminomethyl-2- thiouridine
cmnm5u	5-carboxymethylaminomethyluridine
dhu	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
m4c	N4-methylcytosine
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
m5u	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
OTHER	(requires note qualifier)

Reproduced from WIPO Standard ST. 26, Annex I, Section 2.

IV. JOINTLY DESCRIBING A REGION OF A NUCLEOTIDE SEQUENCE

WIPO Standard ST.26, paragraph 22, specifies that a region containing a known number of contiguous “a”, “c”, “g”, “t”, or “n” residues for which the same description applies may be jointly described using a single INSDFeature element with the syntax “x..y” as the location descriptor in the element INSDFeature_location. See MPEP § 2413.01(g) subsection IV, for information regarding INSDFeature_location. For representation of sequence variants, i.e., alternatives, deletions, insertions or substitutions, see MPEP § 2412.05(c) and MPEP § 2413.01(g), subsection XI.

2412.05(c) Representation and Inclusion of Variants [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/standards/en/pdf/03-26-01.pdf.]

A primary sequence and any variant of that sequence, each disclosed by enumeration of its residues and meeting the definition in 37 CFR 1.831(a) and 1.831(b), must each be included in the “Sequence Listing XML” and assigned its own sequence identifier. Where a variant sequence is disclosed as a single sequence with enumerated alternative residues at one or more positions, it must be included in the “Sequence Listing XML” and should be represented by a single sequence, wherein the enumerated alternative residues are represented by the most restrictive ambiguity symbol. Any variant sequence, disclosed only by reference to deletion(s), insertion(s), or substitution(s) in a primary sequence, should be included in the “Sequence Listing XML”. The table below indicates the proper use of feature keys and qualifiers for nucleic acid and amino acid sequence variants:

List of Feature Keys and Qualifiers

Type of sequence	Feature Key	Qualifier	Use
Nucleic acid	variation	replace or note	Naturally occurring mutations and polymorphisms, e.g., alleles, RFLPs.
Nucleic acid	misc_difference	replace or note	Variability introduced artificially, e.g., by genetic manipulation or by chemical synthesis.
Amino acid	VAR_SEQ	note	Variant produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
Amino acid	VARIANT	note	Any type of variant for which VAR_SEQ is not applicable.

Reproduced from paragraph 96 of WIPO Standard ST.26.

For additional information about feature keys and qualifiers, see MPEP § 2413.01(g), subsections II, III and V.

For additional information about the representation of sequence variants in a “Sequence Listing XML,” see MPEP § 2413.01(g), subsection XI.

2412.05(d) Representation and Symbols of Amino Acid Sequence Data [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/standards/en/pdf/03-26-01.pdf.]

I. REPRESENTATION OF AN AMINO ACID SEQUENCE

WIPO Standard ST.26, paragraph 24, specifies that the amino acids in an amino acid sequence must be represented in the amino to carboxy direction from left to right. The amino and carboxy groups must not be represented in the sequence.

WIPO Standard ST.26, paragraph 25, indicates that the first amino acid in the sequence is residue position number 1, including amino acids preceding the mature protein, for example, pre-sequences, pro-sequences, pre-pro-sequences and signal sequences. When an amino acid sequence is circular in configuration and the ring consists solely of amino acid residues linked by peptide bonds, i.e., the sequence has no amino and carboxy termini, applicant must choose the amino acid in residue position number 1. Numbering is continuous through the entire sequence in the amino to carboxy direction.

II. SYMBOLS FOR AN AMINO ACID SEQUENCE

WIPO Standard ST.26, paragraph 26, specifies that all amino acids in a sequence must be represented using the symbols set forth in Table 3: List of Amino Acids Symbols, in MPEP § 2412.03(a) above. Only uppercase letters must be used. Any symbol used to represent an amino acid is the equivalent of only one residue.

WIPO Standard ST.26, paragraph 27, indicates that where an ambiguity symbol (representing two or more amino acids in the alternative) is appropriate, the most restrictive symbol should be used, as listed in Table 3: List of Amino Acids Symbols (MPEP § 2412.03(a)). For example, if an amino acid in a given position could be aspartic acid or asparagine, the symbol “B” should be used, rather than “X”. The symbol “X” will be construed as any one of “A”, “R”, “N”, “D”, “C”, “Q”, “E”, “G”, “H”, “I”, “L”, “K”, “M”, “F”, “P”, “O”, “S”, “U”, “T”, “W”, “Y”, or “V”, except where it is used with a further description in the feature table. The symbol “X” must not be used to represent anything other than an amino acid. A single modified or “unknown” amino acid may be represented by the symbol “X”, together with a further description in a feature table (see MPEP § 2413.01(g), subsection I or MPEP § 2412.03(c), for more detail regarding a “feature table”). For representation and inclusion of sequence variants, see MPEP § 2412.05(c). For details of how to represent variants in a “Sequence Listing XML,” see MPEP § 2413.01(g), subsection XI.

WIPO Standard ST.26, paragraph 28, specifies that disclosed amino acid sequences separated by internal terminator symbols, represented for example by “Ter” or asterisk “*” or period “.” or a blank space, must be included as separate sequences for each enumerated amino acid sequence that contains at least four specifically defined amino acids and is encompassed by the description of sequences found in MPEP § 2412.03. Each such separate sequence must be assigned its own sequence identifier (see MPEP § 2412.05(a)). Terminator symbols and spaces must not be included in a sequence contained in a “Sequence Listing XML”.

Any “unknown” amino acid must be represented by the symbol “X” in the sequence. An “unknown” amino acid designated as “X” must be further described in a feature table (see MPEP § 2413.01(g), subsection I, for more detail regarding a “feature table” ) using the feature key “UNSURE” and optionally the qualifier “note.” The symbol “X” is the equivalent of only one residue (WIPO Standard ST.26, paragraph 32).

III. DESCRIPTION OF MODIFIED AMINO ACIDS WITHIN AN AMINO ACID SEQUENCE

WIPO Standard ST.26, paragraph 29, specifies that modified amino acids, including D-amino acids, should be represented in the sequence as the corresponding unmodified amino acids whenever possible. Any modified amino acid in a sequence that cannot otherwise be represented by any other symbol in Table 3: List of Amino Acids Symbols (see MPEP § 2412.03(a)), i.e., an “other” amino acid, must be represented by “X”. The symbol “X” is the equivalent of only one residue.

WIPO Standard ST.26, paragraph 30, provides that a modified amino acid must be further described in a feature table (see MPEP § 2413.01(g), subsection I, for more detail regarding a “feature table”). Where applicable, the feature keys “CARBOHYD” or “LIPID” should be used together with the qualifier “note”. The feature key “MOD_RES” should be used for other post-translationally modified amino acids together with the qualifier “note”. The feature key “SITE” together with the qualifier “note” should be used when the modified amino acid is not a post-translationally modified amino acid. The value for the qualifier “note” must either be an abbreviation set forth in Table 4: List of Modified Amino Acids (see MPEP § 2412.03(c)), above, or the complete, unabbreviated name of the modified amino acid. The abbreviations set forth in Table 4, or the complete, unabbreviated names must not be used in the sequence itself.

IV. JOINTLY DESCRIBING A REGION OF AN AMINO ACID SEQUENCE

WIPO Standard ST.26, paragraph 34, provides that a region containing a known number of contiguous “X” residues for which the same description applies may be jointly described in one feature key using the syntax “x..y” as the location descriptor in the element INSDFeature_location (see MPEP § 2413.01(g) subsections II-III for information regarding “feature keys” and subsection IV, for information regarding INSDFeature_location). For representation and inclusion of sequence variants, see MPEP § 2412.05(c). For details of how to represent variants in a “Sequence Listing XML,” see MPEP § 2413.01(g), subsection XII.

2412.05(e) Presentation of Special Situations [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b)].

WIPO Standard ST.26, paragraph 35, describes that a sequence disclosed by enumeration of its residues that is constructed as a single continuous sequence from one or more non-contiguous segments of a larger sequence or of segments from different sequences must be included in the “Sequence Listing XML” and assigned its own sequence identifier, as defined in 37 CFR 1.832(a). See MPEP § 2412.05(a).

WIPO Standard ST.26, paragraph 36, describes that a sequence that contains regions of specifically defined residues separated by one or more regions of contiguous “n” or “X” residues, wherein the exact number of “n” or “X” residues in each region is disclosed, must be included in the “Sequence Listing XML” as one sequence and assigned its own sequence identifier.

WIPO Standard ST.26, paragraph 37, describes that a sequence that contains regions of specifically defined residues separated by one or more gaps of an unknown or undisclosed number of residues must not be represented in the “Sequence Listing XML” as a single sequence. Each region of specifically defined residues (as encompassed by the definition in 37 CFR 1.831(a)) must be included in the “Sequence Listing XML” as a separate sequence and assigned its own sequence identifier.