GENESEQ (Derwent Geneseq™)
Subject
Coverage

All nucleotide sequences of 10 or more bases, all amino acid sequences of 4 or more
residues, and probes and primers of any length.

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• Information on nucleic acid and protein sequences extracted from the original (basic)
patent documents published by 58 patent offices worldwide.
• More than 69 million sequence records within the database stem from over 480,000
patents from around the globe.
• Records contain a Clarivate enhanced title from WPINDEX, a concise sequencedescription, an English abstract written especially for GENESEQ by one of Clarivate
experts, patent information, detailed indexing, a feature table, and sequence data.
• For file crossover to WPINDEX, the DWPI accession number is available in all records.

File Size• More than 69.4 million records (06/2024)• More than 47.1 million nucleic acid sequences (06/2024)• More than 22.3 million protein sequences (06/2024)

Coverage

1980-present

Updates

WeeklyLanguage

English

Database
Producer /Supplier

Clarivate
Friars House, 160 Blackfriars Rd.
London SE1 8EZ
United Kingdom
Copyright Holder: Clarivate

Sources

Patents from the 60 patent issuing authorities covered by the
Derwent World Patents Index® (file WPIDS/WPIX/WPINDEX)

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

Cluster• ALLBIB• BIOSCIENCE• CORPSOURCE• HPATENTS• MEDICINE• PATENTS• PHARMACOLOGYSTN Database Cluster information:
https://www.cas.org/support/training/stn/database-clusters
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GENESEQ

Search and Display Field Codes
General Search Fields
Search Field Name
Basic Index (4) (contains single words
from the title (TI), keyword (KW),
description (DESC), organism name
(ORGN), molecule type (MTY), andfeature table (FEAT) fields)

Search
Code
None
or
/BI

Abstract
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

/AB
/AN
/AA
/AA.CNT/AA.PER
/AC
/AD
/AP
/APO
/AY
/CR

Data Entry Date (1)Description (4)Data Update Date (1)Document Type(code and text)
Entry Date (1)Field Availability
Feature Table (4)

/DED
/DESC
/DUPD
/DT
(or /TC)
/ED
/FA
/FEAT

File Segment(code and text)
Inventor
Language
Keyword (4)Molecule Type
Nucleic Acid
Nucleic Acid Count (1)Nucleic Acid Percentage (1)Organism Name (3,4)
Other Source
Patent Assignee (3)/FS

Patent Assignee CodePatent Country(code and text)
Patent Information Type
Patent Number (2)Patent Number Kind Code (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, Original

/IN
/LA
/KW
/MTY
/NA
/NA.CNT/NA.PER
/ORGN
/OS
/PA
(or /CS)
/PACO
/PC
/PIT
/PN
/PNK
/PNO
/PATS
/PSL
/PD
/PY
/PRC
/PRD
/PRDF
/PRN
/PRNO

Display
Codes

Search Examples
S ANAPHYLATOXINS PLANT GENE# AND RNA

TI, KW,
DESC,
ORGN,
MTY, FEATS GLUCOSE/ABS BJP34154/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 WO 2001-BA6/AP
S WOBE000003/APO
S 2002/AYS HTTP://WWW.NCBI.NLM.NIH.GOV/GENE/
10000/CR/CR
S 20190307/DED
S SYNTHASE/DESC
S 20190307/DUPDS PATENT/DT

AB
AN
AA
AA
AA
AI
AI
AI
APO
AI
CR

S 20211030/ED
S AI/FA
S (RNA AND BINDING)/FEATS ?COMBINAT?/FEATS PROTEIN/FSS NS/FSS MILLER/INS ENGLISH/LAS MUTEIN/KWS 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/ORGN
S 2020-A0561Q/OS
S MOLECULAR DYNAMICS/PA

ED
FA
FEAT

S UYHA-N/PACOS WO/PCPACOPI

S “USA9 CORRECTED PATENTAPPLICATION (FROM 2001 ONWARDS)”/PITS WO2002074965/PN
S WO2002074965A2/PNK
S WO200206834/PNO
S WO2002074965/PATS
S 6/PSLS 20030130/PD
S 2003/PY
S FR/PRC
S 20150606/PRD
S 20150608/PRDF
S EP2001-102050/PRN
S DE04447388/PRNO

PI

DED
DESC
DUPD
DT

FS
IN
LA
KW
MTY
NA
NA
NA
ORGN
OS
PA

PI
PI
PNO
PI
PSL
PI
PI
PRAI
PRAI
PRAI
PRAI
PRNO

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GENESEQ

General Search Fields (cont’d)SearchCode

Search Field Name
Priority Year (1)Priority Year, First
Sequence Key

/PRY
/PRYF
/SEQK

Sequence Identity Number (1)Sequence Length (1)Title (4)Update Date (1)

/SEQN
/SQL
/TI
/UP

Search Examples
S 2000-2001/PRY
S 2015/PRYF
S A000007FBFF70702CD23FD26650417EF67
EF9F464A27334A6217 /SEQK
S 337/SEQN
S 150-175/SQLS HYBRIDIZATION ASSAY#/TI
S 20211030/UP

Display
Codes
PRAI
PRAI
SEQK
SEQN
SQL
TI
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.
(4) Fields that allow left truncation

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.
Search Field Name
Application Number Group

SearchCode/APPS

FieldsSearched/AP, /PRN

Search Examples
S US2001-809003/APPS

Display
Codes
AI, PRAI

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4
GENESEQDISPLAY 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.
FormatAAAB
AI (AP) (1)AN
APO (AIO)
CR
DED
DESC
DUPD
DT (TC)
ED
FASTA
FEAT
FS (2)IDENT (2,3)
IN
LA
KW
MTY
ORGN
OS
PA (CS)
PI (PN) (1)
PIT
PNO
PRAI
PRNO
PSL
SCORE (2,3)
SEQ (4)
SEQ3 (4)
SEQK
SEQN
SQL
TI
UP

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

Examples
D AA
D AB
D AI
D AN
D APO
D CR
D DED
D DESCD DUPDD TC
D AN EDD FASTA
D 1 5 10 FEATD FS
D IDENT
D IN
D LA
D KW
D MTY
D ORGN
D OS
D PA
D PI
D PIT
D PNO
D PRAID PRNP
D PSL
D SCORE
D SEQ
D SEQ3
D 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 GETSIM or RUN BLAST first. See page 7, Similarity Search.
(4) Sequences in GENESEQ 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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GENESEQ

Predefined Display and Print Formats
FormatABS
ALIGN (1)
ALIGNG (1)
ALL
IALL
APPS
BIB
IBIB
FASTA
SCAN
SQIDE
SQ3IDE
TRIAL(TRI, SAM,SAMPLE, FREE)
HIT
KWIC
OCC

Content

ExamplesAN, AB
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 a similarity
search (RUN GETSIM, RUN BLAST, or RUN GETSEQ)
AN, ED, UP, DED, DUPD, TI, IN, PA, PACO, LA, DT, PI, PIT, AI, PRAI, FS,
CR, OS, MTY, PSL, DESC, KW, ORGN, AB, SEQN, SQL, SEQK, SEQ,
AA or NA, FEAT
ALL, indented with text labels
AI, PRAI
AN, ED, UP, DED, DUPD, TI, IN, PA, PACO, LA, DT, PI, PIT, AI, PRAI, FS,
CR, OS, MTY, PSL, DESC
(BIB is the default)
BIB, indented with text labels
FASTA format
ED, UP, DED, DUPD, TI, MTY, DESC (random display without answer
numbers)
AN, ED, UP, DED, DUPD, MTY, ORGN, SEQN, SQL, SEQK, SEQ,
AA or NA, FEAT
AN, ED, UP, DED, DUPD, MTY, ORGN, SEQN, SQL, SEQK, SEQ3,
AA or NA, FEAT
AN, TI, MTY, DESC, KW, SQL

D ABS
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 KWICD ALIGNG
D ALL
D L2 1-5 IALL
D APPSD BIB
D IBIB ALIGND FASTAD SCAND SQIDED SQ3IDE
D 1-20 TRI

D OCC(1) Use RUN GETSIM, RUN BLAST or RUN GETSEQ first.

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GENESEQ

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 thespecified field in an answer set.
The SORT command is used to rearrange the search results in either alphabetic or numeric order of thespecified field(s).
Field Name
Abstract
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 Date
Description
Document Type
Entry Date
Feature Table
File Segment
Inventor
Language
KeywordMolecule Type
Nucleic Acid
Nucleic Acid, Count
Nucleic Acid, Percentage
Other Source
Organism Name
Patent Assignee
Patent Country
Patent Information Type
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 Identity Number
Sequence Key
Sequence Length
Similarity Score
Title
Update Date

Field CodeAB
AN
AA
AA.CNT
AA.PERACAD
AP (AI)
APO (AIO)
APPS
AY
CR
DED
DUPD
DESC
DT (TC)
ED
FEAT
FS
IN
LA
KW
MTY
NA
NA.CNT
NA.PER
OS
ORGN
PA
PC
PIT
PN (PI)
PATS
IDENT
PRC
PRD
PRDF
PRN
PRNO
PRY
PRYF
PSL
PD
PY
SEQN
SEQK
SQL
SCORE (3)TI
UP

ANALYZE/
SELECT (1)

SORT

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

Y
Y
N
N
N
Y
Y
Y
Y
N
Y
Y
Y
Y
Y
Y
Y
N
Y
Y
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
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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GENESEQ

Sequence Similarity Searching (BLAST/GETSIM)
The GETSIM and BLAST® run packages are available to search the GENESEQ database for protein andnucleotide sequence data by similarity (homology). BLAST is provided in GENESQ 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 GENESEQ 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 moremismatches• /TSQP for searching nucleotide sequences translated from GENESEQ protein sequences• /TSQNX for searching translated nucleotides form GENESEQ 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.
Note that 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
RUN BLAST L1 /SQM
RUN BLAST L1 /SQDM/SQM (2)/SQDM (2)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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GENESEQ
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 thepercentage values of the maximum score.
In addition, two score values are given, the highest possible score value defining the maximum score whenthe query 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 the percentage
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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9
GENESEQ
2) 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 theentered value.

3) Select a part of the answer set using the percentage identity value, e.g., "100% IDENT".
The generated L-number 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.

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10
GENESEQ
5) Keep the complete answer set with ALL.

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
the hit sequence. Above each alignment the percentage of the BLAST and GETSIM score compared to thequery 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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GENESEQ

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. It is strongly
recommended 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

2. Expectation Value
3. Word Size-e-w

4. Strand
for nucleotides only
5. Matrix
for peptides only-s

T (True), F (False), Default value is T.
If T is set, for peptides the SEG, and for nucleotides the
DUST filter is employed.
Floating point number. (Default is 10)
11 (default) or 7-23 for nucleotides
3 (default) or 2 for peptides
1 (SIN), 2 (COM) or 3 (BOTH)
default value is 3
BLAST
BLOSUM62 (default), BLOSUM80,
BLOSUM45, PAM30, PAM70
GETSIM
BL50 (default), BL62, BL80, MD10, MD20, MD40, OPT5,
P120, P250, VT160-m

6. Gap Penalty-g

7. Gap Extension-x

8. Penalty for nucleotide mismatch
9. Reward for nucleotide match-q-r

Peptides (default): BLAST 11; GETSIM 12
Nucleotides (default): BLAST 5; GETSIM 12
Peptides: BLAST 1; GETSIM 2
Nucleotides (default): BLAST 2; GETSIM 4
BLAST: -3 (default); GETIM: -2 (default)
BLAST: 1 (default); GETSIM: 3 (default)

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GENESEQ

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

BLOSUM50

June 2024222
1
1 (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

Gap Extension

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

PAM250

13
GENESEQ

Searching Sequence Data with the GETSEQ RUN Package
The GETSEQ run package is a tool to search the GENESEQ 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
30 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
GENESEQ 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 30 GENESEQ COPYRIGHT 2021 CLARIVATE ANALYTICS 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 thestart and end point of the matching part of the hit sequence.
=> D HITL5
ANSWER 50 OF 147 GENESEQ COPYRIGHT 2021 CLARIVATE ANALYTICS on STN.
SEQ
SGTTGKPKG=========
Hits at: 413-420 3426-3433 4466-4473

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14
GENESEQ

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 anunspecified amino acid since July 2022 with standard ST.26. If you want to search specifically for an 'X' in thesequence, 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
Three-letter codes for common amino acids
Enclose strings of codes in single quotes and use
dashes to separate codes in strings.
One-letter codes for nucleic acids

LAGLL/SQSP'HIS-LEU-TYR-LEU-GLN-TYR-ILE-ARG-LYS-LEU'/SQSFP'HIS-LEU-TYR-LEU-GLN-TYR-ILE-ARG-LYS-LEU' /SQEPATGAAN/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
and the SEQ3 field with three-letter codes for proteins only.
Type

Definition

SearchCodeQuery Examples

Sequence Exact
ProteinSequence Exact
Family, Protein

Search for sequences that match thequery.
Search for sequences that match thequery and those in which familyequivalent substitution of the query aminoacids occur.
Search for exact answers plus
sequences in which the query sequenceis embedded.
Search for exact sequences,subsequences, and answers in whichfamily-equivalent substitution of the query
amino acids occurs.
Search for sequences that match thequery. Ambiguity codes for nucleic acids
are allowed.
Search for exact answers, plus
sequences in which the query sequenceis embedded. Ambiguity codes for nucleic
acids are allowed.

/SQEP

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

Subsequence,Protein
Subsequence
Family, Protein
Sequence Exact,
Nucleic Acid
Subsequence,
Nucleic Acid

/SQEFP/SQSP

LAGLL/SQSP'ASP-HIS-ALA'/SQSP/SQSFPATCXAWV/SQSFP'THR-ASP-SER-GLU-SER-SER-HIS'/SQSFP/SQEN

ATGAAN/SQEN/SQSN

TGGAGAAGGC/SQSN

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

June 2024(neutral, weakly hydrophobic)(hydrophilic, acid amine)(hydrophilic, basic)(hydrophobic, aromatic)(hydrophobic)(cross-link forming)

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GENESEQ

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

Query Examples[ ]to specify alternate residues[-]

to exclude a specific residue or alternate
residues

NGSLLAGAYAIST[LV]I/SQSP
LGP['VAL-LEU-LYS']/SQSP
LGP[-H]/SQSP
LGP[-'HIS']/SQSFP
LGP[-HL]/SQSP{m}

to repeat the preceding sequence m times(FL){2}/SQSP(CTGA){3}/SQSN
TAA(TAAA){2}/SQSN{m,u} or {m-u}to repeat the preceding sequence m to utimes
to repeat the preceding sequencezero or one time

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? 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 sequencespecifies alternate residues&

to join together sequence expressions or
queries (L#s)

KLK(DLE){1,}/SQSP
KLK(DLE)+/SQS
CATA(CTG){1,}TATT/SQSN^MCGIL/SQS
VCDS^/SQSP
ACDS|KLMP/SQSPSPECIFYING 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

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: or .? or.{0,1} or .{0-1}a gap of zero or one residues

AGA:SRI/SQSFP
AGA.?SRI/SQSFP
AGA.{0,1}SRI/SQSFP
AGA.{0-1}SRI/SQSFP.* or .{0,} or .{0-}a gap of zero or more residue.+ or .{1,} or .{1-}a gap of one or more residues

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
June 2024

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GENESEQ

Sample Records
DISPLAY TRIALDISPLAY SQIDE

June 2024

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GENESEQDISPLAY IALL

June 2024

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GENESEQ

June 2024

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GENESEQDISPLAY FASTADISPLAY SEQ3

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E-mail:June 2024