PATGENE (Patent Genetic Sequence Database)
Subject
Coverage

Nucleotide and amino acid sequence data as submitted by patent applicants to theWorld Intellectual Property Organization (WIPO).

File Type

Bibliographic, sequence

Features

For direct code match or similarity (homology) sequence searching, FIZ Karlsruhe
provides three specialized RUN package options, GETSEQ, GETSIM and BLAST®.
Alerts (SDIs)

Weekly or monthly (weekly is the default)

CAS Registry
Number® Identifiers



SLART



Keep & Share

Structures



RecordContent• Records contain sequence and patent information as given by the patent applicant.
• Each record includes the actual sequence and additional information on the sequence,
e.g., molecule type and organism, and patent information, e.g., publication, applicationand priority data and patent assignees.

File Size• More than 43.5 million records (06/2024)• More than 31.2 million nucleic acid sequences (06/2024)• More than 12.3 million protein sequences (06/2024)

Coverage

August 2001-present

Updates

WeeklyLanguage

English

Database
Producer

FIZ Karlsruhe - Leibniz-Institute for Information Infrastructure
Hermann-von-Helmholtz-Platz 176344 Eggenstein-Leopoldshafen
Phone: +49 7247 808-0
Email: helpdesk@fiz-karlsruhe.de
Copyright Holder

SourcesSequence listings submitted by patent applicants as a formal part of WIPO/PCT
applications.

User Aids• Online Helps (HELP DIRECTORY lists all help messages available)• STNGUIDE

Clusters

•
•
•
•
•
•
•

ALLBIB
BIOSCIENCECORPSOURCE
HPATENTSMEDICINE
PATENTSPHARMACOLOGYSTN Database Cluster information

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PATGENE

Search and Display Field Codes

Fields that allow left truncation are indicated by an asterisk (*).

General Search Fields
SearchField Name

SearchCode

SearchExamplesDisplay
Codes

Basic Index*(contains single words from the title(TI), organism species (ORGN),
molecule type (MTY) andfeature table (FEAT) fields)

Noneor /BIS ANAPHYLATOXINS PLANT GENE# AND RNA

TI,
ORGN,
MTY,
FEAT

Accession Number
Amino Acid
Amino Acid Count (1)Amino Acid Percentage (1)Application Country
Application Date (1)Application Number (2)Application Number, Original
Application Year (1)Cross Reference
Data Entry Date (1)Data Update Date (1)Document Type (code and text)
Entry Date (1)Field Availability
Feature Table*/AN/AA/AA.CNT/AA.PER
/AC
/AD
/AP
/APO
/AY
/CR
/DED
/DUPD
/DT (or /TC)
/ED
/FA
/FEAT

AN
AA
AA
AA
AI
AI
AI
APO
AI
CR
DED
DUPD
DT
ED
FA
FEAT

File Segment (code and text)/FS

Inventor
Molecule Type
Nucleic Acid)
Nucleic Acid Count (1)Nucleic Acid Percentage (1)Organism Name* (3)Patent Assignee (3)Patent Country (code and text)
Patent Number (2)Patent Number, Original
Patent Number Group (2)Patent Sequence Location
Publication Date (1)Publication Year (1)Priority Country
Priority Date (1)Priority Date, First
Priority Number (2)Priority Number, OriginalPriority Year (1)Priority Year, First
Sequence Count

/IN
/MTY
/NA
/NA.CNT/NA.PER/ORGN/PA (or /CS)
/PC
/PN
/PNO
/PATS
/PSL
/PD
/PY
/PRC
/PRD
/PRDF
/PRN
/PRNO
/PRY
/PRYF
/SEQC

Sequence Key
Sequence Identity Number (1)Sequence Length (1)Title*
Update Date (1)

/SEQK
/SEQN
/SQL
/TI
/UP

S 2002060924.37/AN
S (T OR M)/AAS (T OR M OR F OR H)/AA (S) 50-100/AA.CNT
S (T OR M OR F OR H)/AA (S) 25-30/AA.PER
S US/ACS 20011129/AD
S WO2020-CA51103/AP
S WOAU2004/000622/APO
S 2002/AY
S GENBANK/NM 002650/CR
S 20190228/DED
S 20190228/DUPDS PATENT/DT
S 20210528/ED
S AI/FA
S (RNA AND BINDING)/FEATS ?COMBINAT?/FEATS PROTEIN/FSS NS/FSS MOORE/INS RNA/MTYS (G OR C)/NAS (G OR C)/NA (S) 50-100/NA.CNT
S (G OR C)/NA (S) 60-70/NA.PER
S CRASSOSTREA GIGAS/ORGNS MOLECULAR DYNAMICS/PAS WO/PCS WO 2002074961/PN
S WO2020-000099/PNO
S WO 2002074961/PATS
S 6/PSLS 20030130/PD
S 2003/PY
S FR/PRD
S 20150606/PRD
S 20150608/PRDF
S EP2001-102050/PRN
S DE10 200$ 051 727.5/PRNO
S 2000-2001/PRY
S 2015/PRYF
S 15/SEQC
S A0000030BD19782FC1774AF58E4CFFEE7
F0E30588CBA14DCD38C/SEQK
S 337/SEQN
S 150-175/SQLS HYBRIDIZATION ASSAY#/TI
S 20210528/UP(1) Numeric search field that may be searched using numeric operators or ranges.
(2) Either STN or Derwent format may be used.
(3) Search with implied (S) proximity is available in this field.
June 2024

FS
IN
MTY
NA
NA
NA
ORGN
PA
PI
PI
PNO
PI
PSL
PI
PI
PRAI
PRAI
PRAI
PRAI
PRNO
PRAI
PRAI
SEQC
SEQK
SEQN
SQL
TI
UP

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PATGENE

Super Search Fields
Enter a super search code to execute a search in one or more fields that may contain the desired information.
Super search fields facilitate cross-file and multi-file searching. EXPAND may not be used with super search
fields. Use EXPAND with the individual field codes instead.
SearchField Name

SearchCode

FieldsSearched

SearchExamplesDisplay
Codes

Application Number Group/APPS/AP, /PRNS US2001-809003/APPS

AI, PRAIDISPLAY and PRINT Formats
Any combination of formats may be used to display or print answers. Multiple codes must be separated by
spaces or commas, e.g., D L1 1-5 TI AU. The fields are displayed or printed in the order requested.
Hit-term highlighting is available for all fields. Highlighting must be ON during SEARCH to use the HIT, KWIC,
and OCC formats.
FormatContent

ExamplesAA
AI (AP) (1)AN
APO (AIO)
CR
DED
DUPD
DT (TC)
ED
FASTA
FEAT
FS (2)IDENT (2,3)
IN
MTY
ORGN
PA (CS)
PI (PN) (1)
PNO
PRAI
PRNO
PSL
SCORE (2,4)
SEQ (5)
SEQ3 (5)
SEQC
SEQK
SEQN
SQL
TI
UP

Amino Acid table
Application Information
Accession Number
Application Number, Original
Cross Reference
Data Entry Date
Data Update Date
Document Type
Entry Date
Sequence (FASTA format)
Feature Table
File Segment
Percent Identity
Inventor
Molecule Type
Organism Name
Patent Assignee
Patent Information
Patent Number, OriginalPriority Information
Priority Number, Original
Patent Sequence Location
Similarity Score
Sequence (one-letter codes)
Sequence (three-letter codes)
Sequence Count
Sequence Key
Sequence Identity Number
Sequence Length
Title
Update Date

D AA
D 21 2 AI
D AN TI
D APO
D CR
D DED
D DUPDD DT
D AN EDD FASTA
D 1 5 10 FEATD FS
D IDENTD IN
DIS L5 1-10 MTY
D ORGN
D 1-25 PA
D 1-15 PA PI
D PNO
D PRAID PRNO
D PSL
D TI SCORE
D 1-3 TI SEQ
D 1 5 10 TI SEQ3
D SEQCD SEQKD SEQN
D 1-20 SQL
D L7 1-25 TI
D AN TI UP(1) By default, patent numbers, application and priority numbers are displayed in STN format. To display them in Derwent format, enter
SET PATENT DERWENT at an arrow prompt. To reset display to STN format, enter SET PATENT STN.
(2) Custom display only.
(3) Use RUN BLAST first. See page 7, Similarity Search.
(4) Use RUN GETSIM or RUN BLAST first. See page 7, Similarity Search.
(5) Sequences in PATGENE are given according to ST.25 of the WIPO for records published before 2023, and mostly according to ST.26
since 2023.

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PATGENE

Predefined Display and Print Formats
FormatContent

Examples

ALIGN (1)

Alignment as text between query and retrieved sequence in a similarity
search (RUN GETSIM, RUN BLAST, or RUN GETSEQ)
Alignment as image between query and retrieved sequence in asimilarity search (RUN GETSIM, RUN BLAST, or RUN GETSEQ)
AN, ED, UP, DED, DUPD, TI, IN, PA, DT, PI, AI, PRAI, FS, CR, MTY,
PSL, ORGN, SEQC, SEQN, SQL, SEQK, SEQ, AA or NA, FEAT
AI, PRAI
AN, ED, UP, DED, DUPD, TI, IN, PA, DT, PI, AI, PRAI, FS, CR, MTY,PSL (BIB is the default)
BIB, indented with text labels
FASTA format
ALL, indented with text labels
ED, UP, DED, DUPD, TI (random display without answer numbers)
ED, UP, DED, DUPD, MTY, ORGN, SEQC, SEQN, SQL, SEQK, SEQ,
AA or NA, FEAT
ED, UP, DED, DUPD, MTY, ORGN, SEQC, SEQN, SQL, SEQK, SEQ3,
AA or NA, FEAT
TI, MTY, SQL

D ALIGN

Hit term(s) and field(s)Up to 50 words before and after hit term(s) (KeyWord-In-Context)
Number of occurrences of hit term(s) and field(s) in which they occur

D HIT
D KWICALIGNG (1)
ALL
APPS
BIB
IBIB
FASTA
IALL
SCAN
SQIDE
SQ3IDE
TRIAL (TRI, SAM,SAMPLE, FREE)
HIT
KWIC
OCC

D ALIGNG
D ALL
D APPSD BIB
D IBIB ALIGND FASTAD L2 1-5 IALLD SCAND SQIDED SQ3IDE
D 1-20 TRI(1) Use RUN GETSIM, RUN BLAST or RUN GETSEQ first.

SELECT, ANALYZE, and SORT Fields
The SELECT command is used to create E-numbers containing terms taken from the specified field in ananswer set.
The ANALYZE command is used to create an L-number containing terms taken from the specified field in ananswer set.
The SORT command is used to rearrange the search results in either alphabetic or numeric order of thespecified field(s).
Field
Name

Field
Code

ANALYZE/
SELECT (1)Accession Number
Amino Acid
Amino Acid, Count
Amino Acid, Percentage
Application Country
Application Date
Application Number
Application Number, Original
Application Number and Related Application Number
Application Year
Cross Reference
Data Entry Date
Data Update DateAN
AA
AA.CNT
AA.PERACAD
AP (AI)
APO (AIO)
APPS
AY
CR
DED
DUPD

N
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y

June 2024

SORT
Y
N
N
N
Y
Y
Y
Y
N
Y
Y
Y
Y

5
PATGENE

SELECT, ANALYZE, and SORT Fields (cont’d)
Field
Name

Field
Code

ANALYZE/
SELECT (1)Document Type
Entry Date
Feature Table
File Segment
Inventor
Molecule Type
Nucleic Acid
Nucleic Acid, Count
Nucleic Acid, Percentage
Organism Name
Patent Assignee
Patent Country
Patent Number
Patent Number Group
Percent Identity
Priority Country
Priority Date
Priority Date, First
Priority Number
Priority Number, OriginalPriority Year
Priority Year, First
Patent Sequence Location
Publication Date
Publication Year
Sequence Count
Sequence Identity Number
Sequence Key
Sequence Length
Similarity Score
Title
Update Date

DT (TC)
ED
FEAT
FS
IN
MTY
NA
NA.CNT
NA.PER
ORGN
PA
PC
PN (PI)
PATS
IDENT
PRC
PRD
PRDF
PRN
PNRO
PRY
PRYF
PSL
PD
PY
SEQC
SEQN
SEQK
SQL
SCORE (3)
TI
UP

Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
Y
Y
Y (2)
Y
Y
Y
Y (2)
Y
Y
Y
Y
Y
Y
Y
N
Y (default)
Y

SORT
Y
Y
N
Y
Y
Y
N
N
N
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y

(1) HIT may be used to restrict terms extracted to terms that match the search expression used to create the answer set, e.g.,
SEL HIT PA.
(2) SELECT HIT and ANALYZE HIT are not valid with this field.
(3) Used with a L-number created with BLAST and GETSIM.

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PATGENE

Sequence Similarity Searching (BLAST/GETSIM)
The GETSIM and BLAST® run packages are available to search the PATGENE database for protein andnucleotide sequence data by similarity (homology). BLAST is provided in PATGENE with the permission of the
National Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM). GETSIM isusing the FASTA algorithm.
Nucleotide and protein sequences can be subjected to a similarity search as a query entered directly on thecommand line using RUN GETSIM/BLAST or they may be uploaded via the “Structures” page. See details
here. The uploaded sequence can be displayed with D LQUE.
To initiate a BLAST or GETSIM search with the command RUN BLAST or RUN GETSIM the following search
codes have to be specified:• /SQP for searching peptide sequences• /SQN for nucleotide sequences• /TSQN for searching peptide sequences translated from PATGENE nucleotide sequences.
For the BLAST package four additional search codes are available:• /SQM (megaBLAST) for searching highly similar nucleotide sequences• /SQDM (discontiguous megaBLAST) for searching similar nucleotide sequences allowing more mismatches• /TSQP for searching nucleotide sequences translated from PATGENE protein sequences• /TSQNX for searching translated nucleotides form PATGENE protein sequences
It is recommended to use the search codes /SQM or /SQDM rather than /SQN when searching longer
sequences as the response time is much faster. The commands /TSQN, /TSQP and /TSQNX are more time
consuming compared to the other commands.
When using the /SQN, /SQM, /SQDM, or /TSQNX option, it is possible to specify whether single (SIN),
complementary (COM), or BOTH strands should be searched. The options can be specified with the searchcode, e.g., /SQN -S COM. If no search option is given, BOTH (both) will be used by BLAST and GETSIM. Notethat for the /TSQN option generally both strands will be searched.

GETSIM / BLAST: Types of Searches
Description

Search CodeSearch Examples (1)Peptide homology/SQP

RUN BLAST L1 /SQPRUN GETSIM L1/SQP

Nucleotide homology/SQN

RUN BLAST L1 /SQN
RUN GETSIM L1/SQN/SQM (2)RUN BLAST L1 /SQM

/SQDM (2)RUN BLAST L1 /SQDM

Translated peptide homology/TSQN

RUN BLAST L1 /TSQN
RUN GETSIM L1 /TSQN

Translated peptide homology fromtranslated peptide/TSQNX (2)RUN BLAST L1/TSQNXTranslated nucleotide homology/TSQP (2)RUN BLAST L1 /TSQP(1) Where L1 is a sequence query generated using the “Structure” page. (2) BLAST only

The maximum number of hits is by default 15,000 records. The parameter "-maxseq" allows to increase themaximum number of hits to 100,000 records, e.g.,=>RUN BLAST L1/SQN -F F -MAXSEQ 100000.
The number of additional results and their relevance in terms of high score and/or high identity values dependon the length of the query sequence and the number of subject sequences in the database.
In general, searching a short sequence with -maxseq 100000 may retrieve additional documents with highscore and high identity values while searching a longer sequence with -maxseq 100000 may retrieve only
additional documents with high identity values.

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PATGENE
After a search with BLAST or GETSIM the number of retrieved sequences for the different score values are
displayed in two diagrams. The y-axis of these diagrams represents the number of answers (absolute values
are displayed as bars, logarithmic values are shaded) and the x-axis the score as the specific degree ofsimilarity for this search. In the left diagram the score values are displayed, in the right diagram the percentage
values of the maximum score.
In addition, two score values are given, the highest possible score value defining the maximum score when thequery is aligned to itself, and the score of the best answer of the retrieved answer set. Both values are thesame, if the query and at least one retrieved sequence are identical.

Multiple answer sets (L-numbers) can be created with different cut off values for the score and thepercentage identity. Five options are available:
1) Select a part of the answer set using the score value from the left histogram. The generated L-number
contains all records with a score above the entered value.

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8
PATGENE2) Select a part of the answer set using the percentage score value from the right histogram, e.g., "85%" or"85% SCORE". The generated L-number contains all records with a percentage score above the enteredvalue.

3) Select a part of the answer set using the percentage identity value, e.g., "100% IDENT". The generated Lnumber contains all records with a percentage identity above the entered value.

4) Select a part of the answer set combining the percentage score and the percentage identity value, e.g.,"85% SCORE 100% IDENT". The generated L-number contains all records which have a percentage scoreand percentage identity above the entered value.

5) Keep the complete answer set with ALL.

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9
PATGENE
The percentage score or identity cut off value can be set to two digits after the period. Small differences in the
cut off value can have a tremendous effect on the number of results like in this example:
ENTER (ALL) OR ?:99.45%
L281292 MFPTIPLSRLFDNAMLRAHRLHQLAFDTYQEFEEAYIPKEQKYSFLQNP…
ENTER (ALL) OR ?:99.46%
L29
79 MFPTIPLSRLFDNAMLRAHRLHQLAFDTYQEFEEAYIPKEQKYSFLQNP…

In order to complete the RUN BLAST or the RUN GETSIM command, END must be entered.

An L-number is generated for each selection, which contains all answers of the specified subset. Each
L-number can be used for further processing. As the initial L-number is sorted by descending accession
number, the selected L-number may be re-arranged by descending similarity score (SORT SCORE D L1) ordescending percent identity (SORT IDENT D L1).
The alignment between the retrieved sequence and the query sequence can be displayed as text with thedisplay format ALIGN or as an image with ALIGNG. The top line is the query sequence and the bottom line thehit sequence. Above each alignment the percentage of the BLAST and GETSIM score compared to the query
self-score value and the percentage of identity is given. Both values can also be displayed as well with D
SCORE and D IDENT. Both BLAST and GETSIM ALIGN format follows the standard convention for NCBIalignment displays. See further details in HELP ALIGNMENT.

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PATGENE

Advanced User Options for BLAST and GETSIMFor the experienced user of BLAST® and GETSIM a variety of options are available via the STN commandline. Altering these parameters will have a profound effect on the outcome of the search. FIZ Karlsruhe
strongly recommends that users are completely familiar with NCBI documentation before embarking on
customizing any of these settings. For further information see the information on the NCBI website.
The advanced user options are specified with a single letter code preceded by a hyphen and followed by ablank and the required value, e.g., RUN BLAST L1/SQN -F F or RUN BLAST L1/SQP -E 0.1 -M PAM30.
Advanced User Options
OptionSwitchValues

1. Filter-f

T (True), F (False), Default value is T.
If T is set, for peptides the SEG, and for nucleotides the
DUST filter is employed.

2. Expectation Value-eFloating point number. (Default is 10)

3. Word Size-w

11 (default) or 7-23 for nucleotides
3 (default) or 2 for peptides

4. Strand
for nucleotides only-s

1 (SIN), 2 (COM) or 3 (BOTH)
default value is 3

5. Matrix
for peptides only-m

BLAST: BLOSUM62 (default), BLOSUM80, BLOSUM45,
PAM30, PAM70
GETSIM: BL50 (default), BL62, BL80, MD10, MD20,
MD40, OPT5, P120, P250, VT160

6. Gap Penalty-gPeptides (default): BLAST 11; GETSIM 12
Nucleotides (default): BLAST 5; GETSIM 12

7. Gap Extension-x

Peptides (default): BLAST 1; GETSIM 2
Nucleotides (default): BLAST 2; GETSIM 4

8. Penalty for nucleotide mismatch-q

BLAST: -3 (default); GETIM: -2 (default)

9. Reward for nucleotide match-r

BLAST: 1 (default); GETSIM: 3 (default)

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PATGENE

BLAST Matrix settings (for option 5. Matrix)
Please note that for a certain matrix only a restricted set of possible gap and gap extension values are
possible. The settings available to each matrix are summarised in the table below. Default settings areindicated in the table. Any different combinations will be rejected by the system and a warning message
issued.
MatrixGap

Gap Extension

BLOSUM62

9
8
7
12
11
10

BLOSUM80

8
7
6
11
10
9
13
11
12
9
15
14
13
12
19
18
17
16
32767
13
12
11
10
9
16
15
14
13
12
19
18
17
16
15

BLOSUM45

BLOSUM50222
11 (default)
1
2
2
2
1
1 (default)
1
3
3
3
3
2 (default)
2
2
2
1
1
1
1
32767
3
3
3
3
3
2
2
2
2 (default)
2
1
1
1
1
1

MatrixGap

BLOSUM90

32767
9
8
7
6
11
10

32767
2
2
2
2
1
1 (default)

PAM30

9
7
6
5
10
8
9
8
7
6
11
10
9
32767
15
14
13
12
11
17
16
15
14
13
21
20
19
18
17

1
2
2
2
1
1
1 (default)22211 (default)
1
32767
3
3
3
3
3
2
2
2
2 (default)
2
1
1
1
1
1

PAM70

PAM250Gap Extension

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PATGENE

Searching Sequence Data with the GETSEQ RUN Package
The GETSEQ run package is a tool to search the PATGENE database for a direct sequence code match of
peptide and nucleic acid sequences. This method is ideal for short and/or highly conserved sequence queries
where similarity (homology) searching is not required. The maximum number of hits is 250,000 records.
Nucleotide and protein sequences can be subjected to a GETSEQ search as a query entered directly on thecommand line using RUN GETSEQ or the query may be created with the QUERY command, andsubsequently searched through the GETSEQ run package specifying the query L-number (e.g., RUN GETSEQ
L1, if L1 represents the sequence query).
=> RUN GETSEQ MCLHFLVLVICIL/SQSPRUN GETSEQ AT 08:57:25 ON 2021-10-11
COPYRIGHT (C) 2021 FIZ KARLSRUHE on STN
GetSeq motif search by FIZ Karlsruhe; Version: 1.0.0
Query time:
115
L13
RUN STATEMENT CREATED
L13
8 MCLHFLVLVICIL/SQSPLong sequences may be uploaded via the “Structures” page; see details here. The L-number may also derivefrom a previous sequence search in another STN database with bio sequence search capabilities, e.g., the
CAS REGISTRYSM file.
Any L-numbered sequence answer set from RUN GETSEQ may be combined with any search field in the
PATGENE file, for example => S L1 AND ARTIFICIAL SEQUENCE/ORGN where L1 represents the answer
set from a RUN GETSEQ operation.
Hits of the retrieved sequence can be displayed in context of the whole sequences as text with the display
format ALIGN or as an image with ALIGNG.
=> D ALIGNL3ANSWER 1 OF 8 PATGENE COPYRIGHT 2021 FIZ KARLSRUHE on STN.
ALIGN
Sequence Length: 43;
Hits at: 8-20
1 MFTIRSRMCL HFLVLVICIL RECESVCVCV CVCVCLWHLG RVV=== ==========The HIT display format contains only the part of the hit sequence with the matching residues which arehighlighted with double underlining. In addition, the information HITS AT: gives the residue number of the startand end point of the matching part of the hit sequence.
=> D HITL5
ANSWER 50 OF 147 PATGENE COPYRIGHT 2021 FIZ KARLSRUHE on STN.
SEQ
SGTTGKPKG=========
Hits at: 413-420 3426-3433 4466-4473

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PATGENE

Sequence Search Terms
Amino acid and nucleic acid sequences may be searched with the one-letter code, amino acids also with thethree-letter codes for common amino acids. Enter HELP AAC for a table of the one- and three-letter codes of
the common amino acids and HELP NUC for a table of the codes for nucleic acids.
Uncommon amino acids are represented in the sequence by an 'X' (or 'Xaa'). ‘X’ is used also as an unspecified
amino acid since July 2022 with standard ST.26. If you want to search specifically for an 'X' in the sequence, it
has to be placed in square brackets, e.g., =>RUN GETSEQ TF[X]C[X]T/SQSP
Terms

Search Examples

One-letter codes for common amino acids

LAGLL/SQSPThree-letter codes for common amino acids
Enclose strings of codes in single quotes and use
dashes to separate codes in strings.

'HIS-LEU-TYR-LEU-GLN-TYR-ILE-ARG-LYS-LEU'/SQSFP'HIS-LEU-TYR-LEU-GLN-TYR-ILE-ARG-LYS-LEU' /SQEP

One-letter codes for nucleic acids

ATGAAN/SQEN
CATCTGTATT/SQSN

Types of Sequence Searches
In the GETSEQ run package four options are available for searching polypeptide sequences using amino acidcodes and two options for searching nucleic acid sequences.
Sequence data for nucleic acid and protein sequences are displayed in the SEQ field with one-letter codes andthe SEQ3 field with three-letter codes for proteins only.
Type

Definition

SearchCodeQuery Examples

Sequence Exact
ProteinSequence Exact
Family, Protein

Search for sequences that match the query.

/SQEP

Search for sequences that match thequery and those in which family-equivalent
substitution of the query amino acids occur.
Search for exact answers plus sequences inwhich the query sequence is embedded.
Search for exact sequences, subsequences,
and answers in which family-equivalent
substitution of the query amino acids occurs.
Search for sequences that match the query.
Ambiguity codes for nucleic acids areallowed.
Search for exact answers, plus sequences inwhich the query sequence is embedded.
Ambiguity codes for nucleic acids areallowed.

/SQEFPGAPGEK/SQEP'ASP-HIS-ALA-ILE-HIS' /SQEPYGGFL/SQEFP'TYR-GLY-GLY-PHE-LEU'/SQEFP

Subsequence,Protein
Subsequence
Family,ProteinSequence Exact,
Nucleic Acid
Subsequence,
Nucleic Acid

/SQSP

/SQEN

LAGLL/SQSP'ASP-HIS-ALA'/SQSPATCXAWV/SQSFP'THR-ASP-SER-GLU-SER-SER-HIS'/SQSFPATGAAN/SQEN/SQSN

TGGAGAAGGC/SQSN/SQSFP

The families of amino acid equivalents retrieved in the polypeptide family searches SQEFP and SQSFP are:
P, A, G, S, T
Q, N, E, D, B, Z
H, K, RF, Y, W
L, I, V, M
C

(neutral, weakly hydrophobic)(hydrophilic, acid amine)(hydrophilic, basic)(hydrophobic, aromatic)(hydrophobic)(cross-link forming)

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PATGENE

Variability Symbols for Sequence Code Match Searches
Variability symbols are allowed in all GETSEQ search options. For more information on specifying variability insequence code match queries, enter HELP SQQ.
Symbol(s)Function

Query Examples[ ]to specify alternate residues[-]

to exclude a specific residue or alternate
residues{m}to repeat the preceding sequence m times{m, u} or {m-u}to repeat the preceding sequence m to utimes
to repeat the preceding sequencezero or one time

NGSLLAGAYAIST[LV]I/SQSP
LGP['VAL-LEU-LYS']/SQSP
LGP[-H]/SQSP
LGP[-'HIS']/SQSFP
LGP[-HL]/SQSP(FL){2}/SQSP(CTGA){3}/SQSN
TAA(TAAA){2}/SQSN
GG(FL){1,2}/SQSP(CTGA){2,4}/SQSNFLRRI(RP)?K/SQSPFLRRI(RP){0,1}K/SQSP
CATG(CGTA){0,1}GGAC/SQSNKLK(WD){0,}N/SQSP
KLK(WD)*N/SQSPCATAA(CTG){0,}TATT/SQSN
KLK(DLE){1,}/SQSP
KLK(DLE)+/SQSP
CATA(CTG){1,}TATT/SQSN^MCGIL/SQS
VCDS^/SQSP
ACDS|KLMP/SQSP? or {0,1} or {0-1}* or {0,} or {0-}to repeat the preceding sequence zero or
more times+ or {1,} or {1-}to repeat the preceding sequence
one or more times^ (Caret)search at the beginning or end of a sequence|&specifies alternate residues
to join together sequence expressions or
queries (L#s)

SPECIFYING GAPS IN GETSEQ SEQUENCE QUERIES
A gap may be specified in a sequence expression using the period (.) for one residue, the colon (:) for zero or
one residue or the period (.) followed by an appropriate repeat expression. The following table summarizes all
the options for specifying gaps in GETSEQ sequence searches.
Symbol(s)Function

Query Examples.

a gap of one residue{m} or [m.]a gap of m residues{m,u} or .{m-u}a gap of m to u residues: or .? or.{0,1} or .{0-1}a gap of zero or one residues* or {0,} or .{0-}a gap of zero or more residues+ or {1,} or {1-}a gap of one or more residues

SY.RPG/SQSPSY..RPG/SQSP
AAG...TGC/SQSN
SY.{2}RPG/SQSP
SY[2.]RPG/SQSP
GFF.{2,10}LSS/SQSP
GFF.{2-10}LSS/SQSP
AAG.{2,5}TGC/SQSN
AGA:SRI/SQSFP
AGA.?SRI/SQSFP
AGA.{0,1}SRI/SQSFP
AGA.{0-1}SRI/SQSFP
HLC.*TYG/SQSP
HLC.{0,}TYG/SQSP
HLC.{0-}TYG/SQSP
AAGGCAGATG.*GCAA/SQSN
SY.+TH/SQSP
SY.{1,}TH/SQSP
SY.{1-}TH/SQSP
TCCTG.+GTGG/SQSN

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PATGENE

Sample Records
DISPLAY TRIALDISPLAY SQIDE

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PATGENEDISPLAY IALL

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PATGENEDISPLAY FASTADISPLAY SEQ3

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June 2024