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© FIZ Karlsruhe, January 2012 Robert Austin FIZ Karlsruhe Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany Phone: +49 7247 808 555 Fax: +49 7247 808 259 www.fiz-karlsruhe.de BLAST ® is a registered trademark of the U.S. National Library of Medicine. Page 2 | GENESEQ on STN (DGENE) Workshop Manual
Contents DATABASE CONTENT ............................................................................................................................................. 5 DATABASE CONTENT ........................................................................................................................................................... 6 INTRODUCTION TO SIMILARITY SEARCHING ........................................................................................................ 11 SIMILARITY SEARCHING ..................................................................................................................................................... 12 HOW TO USE GETSIM AND BLAST .................................................................................................................................... 14 SIMILARITY SEARCHING WITH BLAST ................................................................................................................................... 20 SIMILARITY SEARCHING WITH GETSIM ................................................................................................................................ 32 SIMILARITY SEARCHING AND FSORT .................................................................................................................................... 40 ADVANCED SIMILARITY SEARCHING .................................................................................................................... 45 SIMILARITY SEARCHING IN DGENE ...................................................................................................................................... 46 BLAST ADVANCED OPTIONS ............................................................................................................................................... 49 ALTERING BLAST PARAMETERS .......................................................................................................................................... 51 SORTING BY BLAST PERCENT IDENTITY (IDENT) .................................................................................................................... 68 TRANSLATED PROTEIN SIMILARITY SEARCH ............................................................................................................................. 74 BATCH SEARCH MODE ...................................................................................................................................................... 79 CURRENT AWARENESS ALERT SEARCHING ............................................................................................................................. 83 TEXT AND BIBLIOGRAPHIC SEARCHING ................................................................................................................ 87 INTRODUCTION ................................................................................................................................................................ 88 REFINING A BLAST SEARCH WITH TEXT OR DATE TERMS ........................................................................................................... 92 SEQUENCE CODE MATCH SEARCHING ................................................................................................................ 101 SEQUENCE CODE MATCH SEARCHING ................................................................................................................................ 102 GETSEQ SEARCH OPTIONS .............................................................................................................................................. 105 USING VARIABILITY SYMBOLS ............................................................................................................................................ 117 COMPLEMENTARY NUCLEIC ACID SEARCHING ...................................................................................................................... 120 APPENDICES ...................................................................................................................................................... 123 I: AMINO ACID CODES .................................................................................................................................................... 124 II: NUCLEOTIDE CODES .................................................................................................................................................... 126 III: UNIVERSAL GENETIC CODE TABLE ................................................................................................................................. 127 IV: FEATURE KEYS IN DGENE FEATURE TABLES .................................................................................................................... 128 V: MOLECULE TYPE CODES .............................................................................................................................................. 132 VI: DGENE SEARCH AND DISPLAY FIELDS ............................................................................................................................ 133 VII: VARIABILITY SYMBOLS FOR GETSEQ ........................................................................................................................... 135 VIII: BLAST ADVANCED OPTIONS ...................................................................................................................................... 137 IX: SEQUENCE SEARCH QUERY LIMITS ................................................................................................................................ 139 GENESEQ on STN (DGENE) Workshop Manual | Page 3
Page 1: GENESEQ TM STN ® WORKSHOP MANUAL
Page 5 and 6: DATABASE CONTENT In this section, y
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
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 and 92:
Sorting answer sets Text and Biblio
Page 93 and 94:
Prepare and save the query Prepare
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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