Multifile Patent Sequence Searching on STN. Robert Austin FIZ Karlsruhe

Transcription

1 Multifile Patent Sequence Searching on STN Robert Austin FIZ Karlsruhe

2 Agenda Sequence searchable databases on STN Step-by-step through a multifile BLAST search Multifile post-processing using STN Express Overview of the search results Summary and resources See also: Sequence Basics e-seminar (June 2010): 2

3 STN sequence searchable databases DGENE Thomson Reuters GENESEQ TM Value-added patent sequence data from around the globe USGENE The USPTO Genetic Sequence Database All available sequence data from the USPTO PCTGEN WIPO/PCT Patent 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

4 DGENE, USGENE and PCTGEN offer three sequence search modes Sequence 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

5 CAS REGISTRY/CAplus offers two sequence search modes Sequence Code Match (motif) searching Using the Search (=> S) command BLAST similarity Using a separate Graphic User Interface Note: this e-seminar covers BLAST. 5

6 Multifile patent sequence searching Search Question: Find all patents that disclose Homo sapiens D- amino-acid oxidase (NCBI NP_001908), or similar sequences ( 80%): MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLS DPNNPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGF RKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVA REGADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPY IIPGTQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPV RPQIRLEREQLRTGPSNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLSRM PPSHL (Search conducted on 7 th July 2010) 6

7 Multifile 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

8 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

9 SAVE, UPLOAD and VERIFY the query (cont.) (a) Click Upload Sequence (b) Choose the query file (c) Select the STN database (a) (b) (c) From the Discover! button menu. The sequence becomes a Query L-number in the database of choice for use with RUN BLAST. 9

10 SAVE, UPLOAD and VERIFY the query (cont.) => FILE USGENE => UPL R BLAST Commands in red are automatically run by the STN Express Sequence Query Upload wizard. Uploading C:\....\NP_ 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

11 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 Add BATCH to the end of a RUN BLAST command to search in offline batch search mode. PLEASE ENTER BATCH IDENTIFIER (MAX. 8 CHARS):DAOP TO BE NOTIFIED WHEN THIS BATCH SEARCH IS COMPLETE, PLEASE ENTER YOUR 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 New! Enter a valid address to be notified when the BATCH search is completed. 11

12 RUN the DGENE, USGENE and PCTGEN BLAST searches in BATCH mode (cont.) => FILE USGENE => RUN BLAST L1 /SQP -F F BATCH.... PLEASE ENTER BATCH IDENTIFIER (MAX. 8 CHARS):DAOP.... Note: DGENE, USGENE and PCTGEN BLAST searches can be run in parallel using BATCH mode. => FILE PCTGEN => RUN BLAST L1 /SQP -F F BATCH.... Turn the Low Complexity Filter off with the syntax: /SQP F F PLEASE ENTER BATCH IDENTIFIER (MAX. 8 CHARS):DAOP.... => LOG H 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

13 Retrieve the BATCH search results => FILE DGENE FILE 'DGENE' ENTERED AT 17:11:25 ON 07 JUL 2010 COPYRIGHT (C) 2010 THOMSON REUTERS => 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, :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

14 Retrieve the BATCH search results (cont.) => FILE USGENE => RUN GETBATCH DAOP.... Use RUN GETBATCH to retrieve completed BATCH search results. 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% L3 RUN STATEMENT CREATED L3 14 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYAD... MPPSHL/SQP.-F F => FILE PCTGEN => RUN GETBATCH DAOP.... 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% L4 RUN STATEMENT CREATED L4 3 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYAD... MPPSHL/SQP.-F F 14

15 Multifile 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 15

16 Merge the results into a single L-number => SET DUPORDER FILE SET COMMAND COMPLETED => DUP IDE L2 L3 L4 SET DUPORER FILE ensures that multifile records merged using DUP IDE are organized by database (file). FILE 'DGENE' ENTERED AT 17:16:56 ON 07 JUL 2010 COPYRIGHT (C) 2010 THOMSON REUTERS 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 PROCESSING COMPLETED FOR L3 PROCESSING COMPLETED FOR L4 L5 36 DUP IDE L2 L3 L4 (INCLUDES 0 SETS OF DUPLICATES) ANSWERS '1-19' FROM FILE DGENE => SOR IDENT D PROCESSING COMPLETED FOR L5 L6 36 SOR L5 IDENT D ANSWERS '20-33' FROM FILE USGENE ANSWERS '34-36' FROM FILE PCTGEN New! 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

17 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 % 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

18 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 SCORE % 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%) 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

19 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 SCORE % of query self score 731 BLASTALIGN Query = 347 letters Length = 347 Score = 728 bits (1879), Expect = 0.0 Identities = 346/347 (99%), Positives = 346/347 (99%) Query: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN MRVVVIGAGVIGLSTALCIHERYHSVLQPL IKVYADRFTPLTTTDVAAGLWQPYLSDPN Sbjct: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLHIKVYADRFTPLTTTDVAAGLWQPYLSDPN Query: 61 NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR Sbjct: 61 NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR Query: 121 ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN Sbjct: 121 ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN Query: 181 CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQ... CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQ Sbjct: 181 CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQ... 19

20 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

21 Use the STN Express 8.4 Patent 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

22 The patent family manager begins by organising the results using FSORT... => FSORT L6.... L7 36 FSO L6 Commands in RED are those issued automatically by the STN Express Patent Family Manager. 11 Multi-record Families Answers 1-33 Family 1 Answers 1-5 Family 2 Answers 6-8 Family 3 Answers 9-10 Family 4 Answers Family 5 Answers Family 6 Answers Family 7 Answers Family 8 Answers Family 9 Answers Family 10 Answers Family 11 Answers Individual Records Answers Non-patent Records FSORT organizes the patent sequence records by Publication, Application, Related, and Priority numbers. In this example, 14 patent family groups (i.e ) are retrieved. 22

23 ...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 A AI WO 2006-AU PRAI AU PSL Disclosure; SEQ ID NO 18 LA English OS [76] CR N-PSDB: AEL25469 PC-NCBI: gi30446 PC-SWISSPROT: P14920 DESC Reporter protein SEQ ID NO:18. SQL 347 SCORE % of query self score 731 IDENT 99% BLASTALIGN Query = 347 letters Length = 347 Score = 726 bits (1873), Expect = 0.0 Identities = 345/347 (99%), Positives = 345/347 (99%) Commands in RED are those issued automatically by the STN Express Patent Family Manager. 23

24 ...and then continues by displaying the 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 SCORE % of query self score 731 IDENT 99% BLASTALIGN Query = 347 letters Length = 347 Score = 726 bits (1873), Expect = 0.0 Identities = 345/347 (99%), Positives = 345/347 (99%) This USGENE hit is in the same family as the DGENE record on the previous slide (FAMILY 7). Query: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN MRVVVIGAGVIGLSTALCIHERYHSVLQPL IKVYADRFTPLTTTDVAAGLWQPYLSDPN Sbjct: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLHIKVYADRFTPLTTTDVAAGLWQPYLSDPN Query: 61 NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR Sbjct: 61 NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR Query: 121 ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN Sbjct: 121 ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN

25 ...and then continues by displaying the family groups in the specified formats (cont.) => DIS L BIB,SQL,SCORE,IDENT,ALIGN L7 ANSWER 34 OF 36 USGENE COPYRIGHT 2010 SEQUENCEBASE CORP on STN AN 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 A AI US DT Patent SQL 347 SCORE % of query self score 731 IDENT 100% BLASTALIGN Query = 347 letters Length = 347 Score = 731 bits (1886), Expect = 0.0 Identities = 347/347 (100%), Positives = 347/347 (100%) This USGENE record is the first of the 3 individual records in the FSORT answer set (L7). Query: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN Sbjct: 1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN Query: 61 NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR Sbjct: 61 NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR

26 Multifile 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 26

27 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

28 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

29 Input the search query Sequences can be input by Copy/paste Read from a file Recall a previously searched sequence within the same session Sequence line numbers do not interfere with the search. 29

30 Select the BLAST program The following programs are most typically run: BLASTn for nucleotides BLASTp for proteins/peptides 30

31 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

32 View results Highlight the result set to be viewed, and click on View Results. 32

33 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

34 Select sequences of interest Sequences 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

35 Get STN Data and Save alignments (.xss) The alignment data is saved in STN Express Saved Sequences (.xss) format. Alignment data needs to be transferred for post-processing. 35

36 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 Multifile 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 37

38 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 L13 12 L12 AND PATENT/DT => TRANSFER L6 PN 1- L14 TRANSFER L6 1- PN : 20 TERMS L15 29 L14 ALL TERMS IN L14 RETRIEVED. => S L13 NOT L15 L16 2 L13 NOT L15 => D BIB HITRN 1-2 The 44 REGISTRY records (L12) correspond to 12 HCAplus patent records (L13). Transfer Publication Numbers (PN) from DGENE/USGENE/PCTGEN (L6) to find corresponding HCAplus records (L15). In this example, 2 additional, highly relevant references have been found by including the REGISTRY/HCAplus search (L16). 38

39 Example: Unique REGISTRY/CAplus result L16 ANSWER 1 OF 2 HCAPLUS COPYRIGHT 2010 ACS on STN AN 2002: 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 A WO 2001-EP PRAI DE A WO 2001-EP12951 W Note: HITRN must be included, IT , 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 Multifile 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 40

41 Access the Table Tool and select the multifile search Transcript file The most recent STN session Transcript is usually listed here. 41

42 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

43 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

44 Review, adjust, and export the table 44

45 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 Multifile 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 46

47 Post-process REGISTRY BLAST alignments Download the post-processing template (.PRF) files used in this seminar: 47

48 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

49 Select the session Transcript and template The most recent STN session Transcript is usually listed here. Option: choose a predefined custom template from a previous project. 49

50 Select the records to be processed L16 is REGISTRY/CAplus additional unique answers. 50

51 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

52 Review, adjust, and export the report 52

53 Overview of search results for Homo sapiens D- amino-acid oxidase unique in (red) SEQs 80% PNs Patent Families* DGENE (1) USGENE (2) PCTGEN (1) REGISTRY (2) NCBI (0) Total Unique (* Patent families = INPADOC Patent Families. Specifically, family records in INPAFAMDB.)

54 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

55 Resources for sequence searching on STN Sequence Searching on STN modular workshop CAS REGISTRY sequence searching resources DGENE Workshop Manual USGENE Workshop Manual USGENE Workshop Manual Multifile Supplement: 55

56 CAS Support and Training: For more information FIZ Karlsruhe Support and Training: