Multifile Patent Sequence Searching on STN - STN International

<strong>Multifile</strong> <strong>Patent</strong> <strong>Sequence</strong> <strong>Searching</strong> on STN ® 

Robert Austin – FIZ Karlsruhe

Agenda 

• <strong>Sequence</strong> searchable databases on STN ® 

• Step-by-step through a multifile BLAST search 

• <strong>Multifile</strong> post-processing using STN Express 

• Overview of the search results 

• Summary and resources 

See also: <strong>Sequence</strong> Basics e-Seminar (June 2010): 

http://www.stn-international.com/<strong>Sequence</strong>_Basics_Seminar.html 

2

STN sequence searchable databases 

• DGENE 

– Thomson Reuters GENESEQ TM 

– Value-added patent sequence data from around the globe 

• USGENE 

– The USPTO Genetic <strong>Sequence</strong> Database 

– All available sequence data from the USPTO 

• PCTGEN 

– WIPO/PCT <strong>Patent</strong> Application Biosequences 

– All available e-published sequence data from WIPO 

• CAS REGISTRY 

– Chemical Abstracts Service (CAS) REGISTRY 

– Worldwide value-added patent and non-patent sequences 

3

DGENE, USGENE and PCTGEN offer three 

sequence search modes 

• <strong>Sequence</strong> Code Match (motif) searching 

– Using the RUN GETSEQ command 

• BLAST similarity 

– Using the RUN BLAST command 

• FASTA similarity 

– Using the RUN GETSIM command 

Note: this e-Seminar covers BLAST. 

4

CAS REGISTRY/CAplus offers two 

sequence search modes 

• <strong>Sequence</strong> Code Match (motif) searching 

– Using the Search (=> S) command 

• BLAST similarity 

– Using a separate Graphic User Interface 

Note: this e-Seminar covers BLAST. 

5

<strong>Multifile</strong> patent sequence searching 

Search Question: 

Find all patents that disclose Homo sapiens Damino-acid 

oxidase (NCBI NP_001908), or 

similar sequences (≥ 80%): 

MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLS 

DPNNPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGF 

RKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVA 

REGADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPY 

IIPGTQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPV 

RPQIRLEREQLRTGPSNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLSRM 

PPSHL 

(Search conducted on 7 th July 2010) 

6

<strong>Multifile</strong> search strategy 

1) RUN BLAST in DGENE, USGENE and PCTGEN 

using offline BATCH mode 

2) Merge, organize by patent family, and display 

DGENE, USGENE and PCTGEN results 

3) Repeat the search using CAS REGISTRY BLAST 

4) Retrieve, identify, and display unique CAS 

REGISTRY BLAST CAplus records 

5) Post-process DGENE, USGENE and PCTGEN 

results using the STN Express Table Tool 

6) Post-process unique REGISTRY BLAST results 

using the BLAST Report Tool 

7

SAVE, UPLOAD and VERIFY the query 

• Prepare and save the query as a plain text file in 

a suitable text editor, e.g. Windows Notepad 

8

SAVE, UPLOAD and VERIFY the query (cont.) 

(a) Click Upload <strong>Sequence</strong> 

(b) Choose the query file 

(c) Select the STN database 

(a) 

From the Discover! button menu. 

(b) 

(c) 

The sequence becomes a Query 

L-number in the database of 

choice for use with RUN BLAST. 

9

SAVE, UPLOAD and VERIFY the query (cont.) 

=> FILE USGENE 

=> UPL R BLAST 

Commands in red are automatically run by the 

STN Express <strong>Sequence</strong> Query Upload wizard. 

Uploading C:\. . . .\NP_001908 Homo sapiens DAO.txt 

UPLOAD SUCCESSFULLY COMPLETED 

L1 GENERATED 

Verify the sequence was uploaded 

=> D L1 LQUE successfully with D LQUE. 

L1 ANSWER 1 USGENE COPYRIGHT 2010 SEQUENCEBASE CORP on STN 

LQUE MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSD 

PNNPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRK 

LTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREG 

ADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPG 

TQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIR 

LEREQLRTGPSNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLSRMPPSHL 

The sequence query is now ready for searching directly in 

DGENE, USGENE, or PCTGEN using the L-number (L1). 

10

RUN the DGENE, USGENE and PCTGEN 

BLAST searches in BATCH mode 

=> FILE DGENE 

FILE 'DGENE' ENTERED AT 17:05:31 ON 07 JUL 2010 

COPYRIGHT (C) 2010 THOMSON REUTERS 

=> RUN BLAST L1 /SQP -F F BATCH 

PLEASE ENTER BATCH IDENTIFIER (MAX. 8 CHARS):DAOP 

TO BE NOTIFIED WHEN THIS BATCH SEARCH IS COMPLETE, 

PLEASE ENTER YOUR EMAIL ADDRESS (MAX. 50 CHARS) OR "NONE" 

INPUT: OR (END):ROBERT.AUSTIN@FIZ-KARLSRUHE.DE 

BLAST Version 2.2 

The BLAST software is used herein with permission of the 

National Center for Biotechnology Information (NCBI) of 

the National Library of Medicine (NLM). . . . 

BATCH PROCESSING STARTED FOR DAOP 

Add BATCH to the end of 

a RUN BLAST command 

to search in offline batch 

search mode. 

New! 

Enter a valid email 

address to be notified 

when the BATCH 

search is completed. 

11

RUN the DGENE, USGENE and PCTGEN 

BLAST searches in BATCH mode (cont.) 



. . . . 


. . . . 

=> FILE PCTGEN 


. . . . 


. . . . 

=> LOG H 

Note: DGENE, USGENE and 

PCTGEN BLAST searches can be 

run in parallel using BATCH mode. 

Turn the Low Complexity Filter off 

with the syntax: /SQP –F F 

Tip: use LOGOFF HOLD (LOG H) 

to be able to return to the same 

STN session within two hours. 

SESSION WILL BE HELD FOR 120 MINUTES 

STN INTERNATIONAL SESSION SUSPENDED AT 17:07:14 ON 07 JUL 2010 

12

Retrieve the BATCH search results 

=> FILE DGENE 



=> RUN GETBATCH DAOP 

Use RUN GETBATCH to retrieve 

Please enter your batch identifier completed BATCH search results. 

or enter # for batch id list 

or enter * for batch id at top of list 

or enter - before batch id to delete 

or enter . for (end) 

Database DGENE AA 

Posted date: Jun 25, 2010 11:33 PM 

. . . . 

ENTER EITHER THE NUMBER OF ANSWERS YOU WISH TO KEEP 

OR ENTER MINIMUM PERCENT OF SELF SCORE FOLLOWED BY % 

(BEST ANSWER PERCENTAGE OF SELF SCORE IS 100%) 

ENTER (ALL) OR ? :80% 

L2 RUN STATEMENT CREATED 

L2 19 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYAD. . . MPPSHL/SQP.-F F 

In this example, 80% of the Query 

Self Score is used to select out 

just the most relevant results (L2). 

Answer set arranged by accession number; to sort by descending 

similarity score, enter at an arrow prompt (=>) "sor score d". 

13

Retrieve the BATCH search results (cont.) 



. . . . 







=> FILE PCTGEN 


. . . . 

Use RUN GETBATCH to retrieve 

completed BATCH search results. 







14













15

Merge the results into a single L-number 

=> SET DUPORDER FILE 

SET COMMAND COMPLETED 

=> DUP IDE L2 L3 L4 



FILE 'USGENE' ENTERED AT 17:16:56 ON 07 JUL 2010 

COPYRIGHT (C) 2010 SEQUENCEBASE CORP 

FILE 'PCTGEN' ENTERED AT 17:16:56 ON 07 JUL 2010 

COPYRIGHT (C) 2010 WIPO 

PROCESSING COMPLETED FOR L2 



L5 36 DUP IDE L2 L3 L4 (INCLUDES 0 SETS OF DUPLICATES) 

ANSWERS '1-19' FROM FILE DGENE 

=> SOR IDENT D 


L6 36 SOR L5 IDENT D 

ANSWERS '20-33' FROM FILE USGENE 

ANSWERS '34-36' FROM FILE PCTGEN 

New! 

SET DUPORER FILE ensures that 

multifile records merged using DUP 

IDE are organized by database (file). 

DUPLICATE IDENTIFY 

(DUP IDE) is used 

here to create a single 

multifile L-number (L5). 

The multifile L-number 

(L5) can be sorted by 

BLAST SCORE, or 

Percent Identity (IDENT). 

16

Review multifile answers with a free-of-charge 

format including alignment 

=> D L6 TRIAL SCORE ALIGN 1-36; FILE STNGUIDE 

L6 ANSWER 1 OF 36 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN 

AN AAO23074 Protein DGENE 

TI Determining a genotype of an individual for preparing a composition 

for treating schizophrenia by determining the identity of a 

nucleotide at a biallelic marker of the D-amino acid oxidase gene of 

the polynucleotide in a sample - 

DESC Human D-amino acid oxidase wild-type protein. 

KW Biallelic marker; D-amino acid oxidase; DAO; neuroleptic; CNS 

disorder; movement; Parkinson's disease; Huntington's; motor 

neurone; Alzheimer's; mood; unipolar depression; bipolar; . . . . 

SQL 347 

Query Self Score 

and percentage. 

SCORE 731 100% of query self score 731 

BLASTALIGN 

Query = 347 letters 

Length = 347 

Score = 731 bits (1886), Expect = 0.0 

Identities = 347/347 (100%), Positives = 347/347 (100%) 

Query: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQP . . . 

MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQP 

Sbjct: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQP . . . 

17

Review answers with a free-of-charge format 

including alignment (cont.) 

L6 ANSWER 4 OF 36 USGENE COPYRIGHT 2010 SEQUENCEBASE CORP on STN 

TI Collections of matched biological reagents and methods for 

identifying matched reagents (PublishedApplication) 

MTY Protein 

SQL 347 


BLASTALIGN 


Length = 347 



BLAST Percent 

Identity (IDENT). 

Query: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN 

MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN 

Sbjct: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN 

Query: 61 NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR 

NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR 

Sbjct: 61 NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR 

Query: 121 ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN 

ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN 

Sbjct: 121 ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN 

Query: 181 CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQ . . . 

CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQ 

Sbjct: 181 CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQ . . . 

18

Review answers with a free-of-charge format 

including alignment (cont.) 

L6 ANSWER 28 OF 36 PCTGEN COPYRIGHT 2010 WIPO on STN 

TI ORGAN-SPECIFIC PROTEINS AND METHODS OFTHEIR USE 

MTY PRT 

SQL 347 


BLASTALIGN 


Length = 347 




MRVVVIGAGVIGLSTALCIHERYHSVLQPL IKVYADRFTPLTTTDVAAGLWQPYLSDPN 

Sbjct: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLHIKVYADRFTPLTTTDVAAGLWQPYLSDPN 







Query: 181 CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQ . . . 

CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQ 

Sbjct: 181 CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQ . . . 

19

Ensure Capture Session is on to record a 

transcript for use in post-processing 

Note: Check the Capture 

Retrospectively box to capture 

the session so far, as well as the 

session from this point forwards. 

20

Use the STN Express 8.4 <strong>Patent</strong> Family 

Manager wizard display the results 

Access the patent family 

manager wizard from the 

Discover! Menu. 

Choose a bibliographic display format with 

alignment for the first (best) hit, and a free-ofcharge 

format with alignment for the rest of 

the sequences in each patent family group. 

21

The patent family manager begins by 

organising the results using FSORT... 

=> FSORT L6 

. . . . 

L7 36 FSO L6 

11 Multi-record Families Answers 1-33 

Family 1 Answers 1-5 











3 Individual Records Answers 34-36 

0 Non-patent Records 

Commands in RED are those 

issued automatically by the STN 

Express <strong>Patent</strong> Family Manager. 

FSORT organizes 

the patent 

sequence records 

by Publication, 

Application, 

Related, and 

Priority numbers. 

In this example, 14 patent family 

groups (i.e. 11 + 3) are retrieved. 

22

...and then continues by displaying the 

family groups in the specified formats 

=> DIS L7 PFAM=7 1 BIB,SQL,SCORE,IDENT,ALIGN 

L7 ANSWER 17 OF 36 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN FAMILY7 

AN AEL25470 protein DGENE 

TI Identifying compound that reduce/inhibit internal ribosome . . . . 

IN Fear M 

PA (TELE-N) TELETHON INST CHILD HEALTH RES. 

PI WO 2006102720 A1 20061005 197 

AI WO 2006-AU435 20060331 

PRAI AU 2005-901574 20050331 

PSL Disclosure; SEQ ID NO 18 

LA English 

OS 2006-747347 [76] 

CR N-PSDB: AEL25469 

PC-NCBI: gi30446 

PC-SWISSPROT: P14920 

DESC Reporter protein SEQ ID NO:18. 

SQL 347 


IDENT 99% 

BLASTALIGN 


Length = 347 



. . . . 

. . . . 

Commands in RED are those 

issued automatically by the STN 

Express <strong>Patent</strong> Family Manager. 

23


family groups in the specified formats (cont.) 

=> DIS L7 PFAM=7 2-TOT TRIAL,SCORE,IDENT,ALIGN 

L7 ANSWER 18 OF 36 USGENE COPYRIGHT 2010 SEQUENCEBASE CORP on STNFAMILY7 

TI Isolation of Inhibitors of IRES-Mediated Translation 

(PublishedApplication) 

DESC Homo Sapiens Protein; sequence 18 of 148 

MTY Protein 

SQL 347 


IDENT 99% 

BLASTALIGN 


Length = 347 



This USGENE hit is in the same 

family as the DGENE record on 

the previous slide (FAMILY 7). 


MRVVVIGAGVIGLSTALCIHERYHSVLQPL IKVYADRFTPLTTTDVAAGLWQPYLSDPN 

Sbjct: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLHIKVYADRFTPLTTTDVAAGLWQPYLSDPN 







. . . . 

24


family groups in the specified formats (cont.) 

=> DIS L7 34-36 BIB,SQL,SCORE,IDENT,ALIGN 

L7 ANSWER 34 OF 36 USGENE COPYRIGHT 2010 SEQUENCEBASE CORP on STN 

AN 20060275794.63099 Protein USGENE 

TI Collections of matched biological reagents and methods for 

identifying matched reagents (PublishedApplication) 

IN Carrino John (San Diego, CA); Liang Feng (San Diego, CA) 

PA Invitrogen Corporation (Carlsbad CA) 

PI US 20060275794 A1 20061207 

AI US 2006-371354 20060307 

DT <strong>Patent</strong> 

SQL 347 


IDENT 100% 

BLASTALIGN 


Length = 347 



This USGENE record is the first 

of the 3 “individual records” in 

the FSORT answer set (L7). 


MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN 

Sbjct: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN 




. . . . 

25













26

Typical steps of CAS REGISTRY BLAST 

1. Launch BLAST 

2. Search the sequence 

3. Examine and evaluate alignment/relevance of 

sequence answers 

4. Display STN data on sequences – REGISTRY 

5. Display STN data on sequences – CAplus SM 

– Limit CAplus results, if necessary 

– Display CAplus data (references and HITRN) 

6. Post-process BLAST alignment data 

27

Launch CAS REGISTRY BLAST 

• The Result Set Manager is 

the starting point 

• To begin a new sequence 

search 

• To review results of previous 

sequence searches 

28

Input the search query 

• <strong>Sequence</strong>s can be input by Copy/paste 

• Read from a file 

• Recall a previously searched sequence 

within the same session 

• <strong>Sequence</strong> line numbers do not 

interfere with the search. 

29

Select the BLAST program 

The following programs are 

most typically run: 

• BLASTn for nucleotides 

• BLASTp for proteins/peptides 

30

Verify BLAST settings 

Default values have been set to 

optimize sequence searches for 

researchers. 

Recommended settings for 

patent searches: 

• Low Complexity Filtering – 

unchecked 

• Max No. of Answers - 1000 

31

View results 

Highlight the result set 

to be viewed, and click 

on View Results. 

32

Evaluate the alignment report 

The negative sign represents 

that the alignment details are 

shown. 

Detail information such as the 

sequence length, score, 

percent identity are available. 

33

Select sequences of interest 

<strong>Sequence</strong>s can be selected: 

• In groups, using the color bar in the 

Alignment Scores 

• Individually, by selecting the check box 

• To transfer the sequence data to STN, 

click the Get STN Data button. 

34

Get STN Data and Save alignments (.xss) 

Alignment data needs 

to be transferred for 

post-processing. 

The alignment data is saved in STN 

Express Saved <strong>Sequence</strong>s (.xss) format. 

35

Transfer sequences to STN 

• Logon to STN and a REGISTRY search 

of the sequences is automatic. 

• Results display can be accomplished 

using either Discover! wizards or 

command line input. 

• Note: Type END or click Cancel to get 

out of the “Display Wizard”. You can turn 

off the “Display Wizard” in Preferences. 

Display sequences if desired. 

36













37

Display additional CAplus answers including 

the HITRN for alignment post-processing 

=> FILE HCAPLUS 

FILE 'HCAPLUS' ENTERED AT 17:25:10 ON 07 JUL 2010 

COPYRIGHT (C) 2010 AMERICAN CHEMICAL SOCIETY (ACS) 

=> S L12 AND PATENT/DT 

The 44 REGISTRY records (L12) 

L13 12 L12 AND PATENT/DT 

correspond to 12 HCAplus patent 

records (L13). 

=> TRANSFER L6 PN 1- 

L14 TRANSFER L6 1- PN : Transfer 20 TERMS Publication Numbers (PN) 

L15 29 L14 

from DGENE/USGENE/PCTGEN 

ALL TERMS IN L14 RETRIEVED. 

(L6) to find corresponding HCAplus 

records (L15). 

=> S L13 NOT L15 

L16 2 L13 NOT L15 

=> D BIB HITRN 1-2 

In this example, 2 additional, highly 

relevant references have been 

found by including the 

REGISTRY/HCAplus search (L16). 

38

Example: Unique REGISTRY/CAplus result 

L16 ANSWER 1 OF 2 HCAPLUS COPYRIGHT 2010 ACS on STN 

AN 2002:391912 HCAPLUS 

DN 137:1836 

TI Measurement of DNA methylation for analysis of the toxicology . . . . 

IN Olek, Alexander; Piepenbrock, Christian; Berlin, Kurt 

PA Epigenomics Ag, Germany 

SO PCT Int. Appl., 113 pp. 

CODEN: PIXXD2 

LA German 

FAN.CNT 1 

PATENT NO. KIND DATE APPLICATION NO. DATE 

--------------- ---- -------- -------------------- -------- 

PI WO 2002040710 A2 20020523 WO 2001-EP12951 20011108 

. . . . 

PRAI DE 2000-10056802 A 20001114 

WO 2001-EP12951 W 20011108 

Note: HITRN must be included, 

IT 391975-30-7, Protein (human 347-amino acid) 

RL: BSU (Biological study, unclassified); so that PRP the (Properties); CAS REGISTRY BIOL 

(Biological study) 

BLAST alignments can be 

(amino acid sequence; measurement of DNA methylation for anal. of 

the toxicol. of substances) 

merged into the BLAST Report. 

39













40

Access the Table Tool and select the 

multifile search Transcript file 

The most recent STN session 

Transcript is usually listed here. 

41

Choose a template and select content 

Option: choose a predefined 

custom template 

from a previous project. 

L7 is the DGENE, 

USGENE and PCTGEN 

FSORTed answer set. 

42

Select fields, column order, headings, fonts 

and spacing for the table 

The pre-defined custom 

template included a list 

of fields. These can be 

further customized and 

the template re-saved. 

43

Review, adjust, and export the table 

44

Explore the results further in Microsoft Excel 

Some tips for Microsoft Excel: 

• Resize columns and rows as desired – 

especially the BLAST alignment 

column to approx 77 

• View, Freeze panes – holds the top row 

fixed when scrolling down 

• Add Filters – provides a great way to 

navigate results – for example by 

BLAST percent identity (above) 

45













46

Post-process REGISTRY BLAST alignments 

Download the post-processing template (.PRF) files used in this seminar: 

http://www.stn-international.com/stn_biosequence_searching_mfs.html 

47

Select BLAST alignment report 

• The first step is to select the XSS 

file to include in the BLAST report. 

• Important: If your BLAST query is 

fairly long, or a nucleic acid, or the 

answers may exceed 1000 

characters, make sure you change 

the value in the Do not include 

alignments longer than box. 

Post-processing then continues 

via standard STN Express 

Custom Report Tool steps. 

48

Select the session Transcript and template 

Option: choose a predefined 

custom template 

from a previous project. 

The most recent STN 

session Transcript is 

usually listed here. 

49

Select the records to be processed 

L16 is REGISTRY/CAplus 

additional unique answers. 

50

Select fields, fonts and spacing for the report 

The pre-defined custom 

template included a list 

of fields. These can be 

further customized and 

the template re-saved. 

51

Review, adjust, and export the report 

52

Overview of search results for Homo sapiens Damino-acid 

oxidase – unique in (red) 

SEQs 

≥ 80% 

PNs 

<strong>Patent</strong> 

Families* 

DGENE 19 10 8 (1) 

USGENE 14 10 7 (2) 

PCTGEN 3 3 3 (1) 

REGISTRY 18 12 9 (2) 

NCBI 6 4 4 (0) 

Total Unique - - 14 

(* <strong>Patent</strong> families = INPADOC <strong>Patent</strong> Families. Specifically, family records in INPAFAMDB.)

Summary 

• RUN BLAST is available for searching DGENE, 

USGENE and PCTGEN directly on STN 

• CAS REGISTRY BLAST provides BLAST searching 

options for the REGISTRY database 

• DGENE, USGENE and PCTGEN multifile search 

results can be post-processed into tables, and 

exported to Microsoft Excel, using STN Express 

• CAS REGISTRY BLAST alignment data can be 

merged with CAplus records, and exported in to RTF 

format, to form single unified report 

• All four STN sequence databases are required for a 

comprehensive patent sequence search 

54

Resources for sequence searching on STN 

• <strong>Sequence</strong> <strong>Searching</strong> on STN modular workshop 

http://www.stn-international.com/sequence_searching.html 

• CAS REGISTRY sequence searching resources 

http://www.cas.org/support/stngen/stndoc/sequences.html 

• DGENE Workshop Manual 

http://www.stn-international.com/dgene_wm.html 

• USGENE Workshop Manual 

http://www.stn-international.com/usgene_wm.html 

• USGENE Workshop Manual <strong>Multifile</strong> Supplement: 

http://www.stn-international.com/usgene_wm_mfs.html 

55

CAS 

E-mail: help@cas.org 

Support and Training: 

www.cas.org 

For more information … 

FIZ Karlsruhe 

helpdesk@fiz-karlsruhe.de 

Support and Training: 

www.stn-international.de

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