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Page 4 | GENESEQ on STN (DGENE) Workshop Manual Sequence databases on STN This Workshop Manual is focused on the content and search features of the Thomson Reuters GENESEQ TM (DGENE) database on STN. Information on the USPTO Genetic Sequence Database (USGENE ® ), World Patent Application Biosequences (PCTGEN), and CAS Registry ® (REGISTRY) are available at the STN International website. <strong>note</strong> USGENE ® STN Workshop Manual: http://www.stn-international.com/usgene_wm.html USGENE Workshop Manual Supplement – Multi-file BLAST searching: http://www.stn-international.com/usgene_wm_mfs.html
DATABASE CONTENT In this section, you will learn about � Database content and coverage � The layout of a typical database record
Page 1 and 2: GENESEQ TM STN ® WORKSHOP MANUAL
Page 3: Contents DATABASE CONTENT .........
Page 7 and 8: How to read a DGENE record Database
Page 9 and 10: Patent family and legal status info
Page 11 and 12: INTRODUCTION TO SIMILARITY SEARCHIN
Page 13 and 14: GETSIM Introduction to similarity s
Page 15 and 16: The uploaded sequence text file bec
Page 17 and 18: Introduction to similarity searchin
Page 21 and 22: Prepare the query offline Prepare y
Page 23 and 24: Sort the answers by descending simi
Page 25 and 26: Display selected answers in a bibli
Page 27 and 28: Prepare the query offline Prepare y
Page 29 and 30: Sort similarity score descending An
Page 33 and 34: 9590 ANSWERS FOUND ABOVE A THRESHOL
Page 37 and 38: RUN GETSIM for a SQN BOTH search In
Page 41 and 42: Upload the sequence and conduct a B
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
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. . . . Advanced similarity searchi
Page 79 and 80:
Batch Search Mode Advanced similari
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Collection of Batch Results Advance
Page 83 and 84:
Current Awareness Alert Searching A
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CURRENT RESULTS AVAILABLE NAME RUN
Page 87 and 88:
TEXT AND BIBLIOGRAPHIC In this sect
Page 89 and 90:
Additional search indexes Text and
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Sorting answer sets Text and Biblio
Page 93 and 94:
Prepare and save the query Prepare
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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
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Protein EXACT Search GETSEQ search
Page 107 and 108:
Protein EXACT FAMILY Search Sequenc
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Protein SUBSEQUENCE Search Sequence
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Protein SUBSEQUENCE FAMILY Search S
Page 113 and 114:
Nucleic acid EXACT Search Sequence
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Nucleic Acid SUBSEQUENCE Search Seq
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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
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Three letter codes 3-Letter Code 1-
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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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