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Text and Bibliographic searching Refining a BLAST search with text or date terms Search Question: Find patent publications with a priority date earlier than 2001, which disclose this human Expressed Sequence Tag (EST), or similar sequence, within the context of the treatment or diagnosis of HIV/AIDS: Page 92 | GENESEQ on STN (DGENE) Workshop Manual CGTTGCTCTGGGATTTCTTTGCTGGATTCCAGACTTTTGCTGTCAGGTAT TGCTTCTTTACTTTCTCCTTTATTAGGTTTTTTTCTTTTCCTCTCCCTTC CTTTTTTTCCTCGTTCTCCCTTCTGACACTTCTTCCTTTGCACTGTACAC TTTCTTGTCTCATTTGTTGGGGGACATAGGTTACCCTTTGCTGAAGGATG CTGTATTATTTCTCGGACCCGTGTTTCAGTCCCTCTTTTGAAGCCACATG TTTTTCCCTTCTTCGTGCATGGACTCCAAGGATTCCATTCACTGACCTCA CAGTGCACAATACTGACACACTCCATAGTATGGTTGTTGGCTTCCAACCC TTCTGGGCAATTGTCAAGGCACTTTCCAAGGTGTAAGTAN Search Strategy To refine a BLAST similarity search with text or date terms… Step 1 Prepare the sequence query offline Step 2 Upload the sequence using STN Express Step 3 Conduct a BLAST search and keep all answers Step 4 Refine the results using various search fields Step 5 Review and display selected answers
Prepare and save the query Prepare your query a text editor, e.g. Windows Notepad. Upload the sequence query text file via STN Express (version 8.2 or higher): Click the Discover! button and select Upload Sequence or Structure to STN A sequence query L-number is generated in DGENE => FILE DGENE FILE 'DGENE' ENTERED AT 14:17:22 ON 28 DEC 2010 COPYRIGHT (C) 2010 THOMSON REUTERS Text and Bibliographic searching Click Browse, pick the text file and click Next to continue Select DGENE and then click Finish => UPL R BLAST Uploading C:\Documents and Settings\Rob Austin\Desktop\EST HIV-AIDS query.txt UPLOAD SUCCESSFULLY COMPLETED L1 GENERATED These commands are automatically run by the STN Express Sequence Query Upload wizard. GENESEQ on STN (DGENE) Workshop Manual | Page 93
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GENESEQ TM STN ® WORKSHOP MANUAL
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Contents DATABASE CONTENT .........
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DATABASE CONTENT In this section, y
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How to read a DGENE record Database
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Patent family and legal status info
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INTRODUCTION TO SIMILARITY SEARCHIN
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GETSIM Introduction to similarity s
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The uploaded sequence text file bec
Page 17 and 18:
Introduction to similarity searchin
Page 19 and 20:
Introduction to similarity searchin
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Prepare the query offline Prepare y
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Sort the answers by descending simi
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Display selected answers in a bibli
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Prepare the query offline Prepare y
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Sort similarity score descending An
Page 31 and 32:
Page 33 and 34:
9590 ANSWERS FOUND ABOVE A THRESHOL
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Page 37 and 38:
RUN GETSIM for a SQN BOTH search In
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Page 41 and 42: Upload the sequence and conduct a B
Page 43 and 44: Introduction to similarity searchin
Page 45 and 46: ADVANCED SIMILARITY SEARCHING In th
Page 47 and 48: RUN BLAST Advanced similarity searc
Page 49 and 50: BLAST advanced options Advanced sim
Page 51 and 52: Altering BLAST parameters Advanced
Page 53 and 54: Sort the answer set according to si
Page 55 and 56: 9913 ANSWERS FOUND BELOW EXPECTATIO
Page 57 and 58: Advanced similarity searching L4 AN
Page 59 and 60: Run a BLAST similarity search with
Page 61 and 62: Display some records with alignment
Page 63 and 64: Protein sequences: switching off th
Page 65 and 66: Sort similarity score descending An
Page 67 and 68: Display selected answers in a bibli
Page 69 and 70: Upload the sequence query text file
Page 71 and 72: Review the answers using IDENT and
Page 73 and 74: Display selected answers in a bibli
Page 75 and 76: RUN GETSIM using the translated (/T
Page 77 and 78: . . . . Advanced similarity searchi
Page 79 and 80: Batch Search Mode Advanced similari
Page 81 and 82: Collection of Batch Results Advance
Page 83 and 84: Current Awareness Alert Searching A
Page 85 and 86: CURRENT RESULTS AVAILABLE NAME RUN
Page 87 and 88: TEXT AND BIBLIOGRAPHIC In this sect
Page 89 and 90: Additional search indexes Text and
Page 91: Sorting answer sets Text and Biblio
Page 95 and 96: 341 ANSWERS FOUND BELOW EXPECTATION
Page 97 and 98: Text and Bibliographic searching Re
Page 99 and 100: Display selected answers in a prefe
Page 101 and 102: SEQUENCE CODE MATCH SEARCHING In th
Page 103 and 104: Sequence Code Match Searching Exact
Page 105 and 106: Protein EXACT Search GETSEQ search
Page 107 and 108: Protein EXACT FAMILY Search Sequenc
Page 109 and 110: Protein SUBSEQUENCE Search Sequence
Page 111 and 112: Protein SUBSEQUENCE FAMILY Search S
Page 113 and 114: Nucleic acid EXACT Search Sequence
Page 115 and 116: Nucleic Acid SUBSEQUENCE Search Seq
Page 117 and 118: Using variability symbols Sequence
Page 119 and 120: Excluding residues Sequence Code Ma
Page 121 and 122: Repeat the search with the compleme
Page 123 and 124: APPENDICES This section includes ap
Page 125 and 126: Three letter codes 3-Letter Code 1-
Page 127 and 128: III: Universal Genetic Code Table A
Page 129 and 130: Nucleic acids Appendices Nucleotide
Page 131 and 132: Appendices Feature Definition termi
Page 133 and 134: Search fields VI: DGENE search and
Page 135 and 136: VII: Variability Symbols for GETSEQ
Page 137 and 138: VIII: BLAST advanced options Parame
Page 139 and 140: IX: Sequence Search Query Limits Ap
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note - FIZ Karlsruhe

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