note - FIZ Karlsruhe

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Appendices Matrix specific gap costs For each matrix 1 which can be used with BLAST /SQP or BLAST /TSQN only a distinct subset of gap existence costs and gap extension costs is accepted (see table below). Matrix Gap Existence Gap Extension 9 2 8 2 7 2 BLOSUM62 12 1 11 1 10 1 (default) 8 2 7 2 6 2 BLOSUM80 11 1 10 1 (default) 9 1 13 3 11 3 12 3 9 3 15 2 (default) 14 2 BLOSUM45 13 2 12 2 19 1 18 1 17 1 16 1 7 2 6 2 5 2 PAM30 10 1 8 1 9 1 (default) 8 2 7 2 6 2 PAM70 11 1 10 1 (default) 9 1 1 http://www.ncbi.nlm.nih.gov/BLAST/matrix_info.html Page 138 | GENESEQ on STN (DGENE) Workshop Manual
IX: Sequence Search Query Limits Appendices STN has general command length limits, and specific query length limits for sequence searching using RUN GETSEQ (page 102), RUN BLAST (page 47) and RUN GETSIM (page 48). DGENE query limits for GETSEQ Sequence Code Match (SCM) searching: � Maximum limit of 256 characters if run online (as for general STN) � Maximum limit of 300 characters if via a COMMAND FILE (as for general STN) � Maximum limit of 2,000 characters as a query text file using UPLOAD (page 14) � Each line within a query text file using UPLOAD must not exceed 300 characters 1 DGENE query limits for BLAST similarity searching: � Maximum limit of 256 characters if run online (as for general STN) � Maximum limit of 300 characters if via a COMMAND FILE (as for general STN) � Maximum limit of 10,000 characters as a query text file using UPLOAD (page 14), for online, BATCH and ALERT searches in all search modes (/SQP, /SQN or /TSQN) � Each line within a query text file using UPLOAD must not exceed 300 characters 1 DGENE query limits for GETSIM similarity searching: � Minimum limit of 5 characters � Maximum limit of 256 characters if run online (as for general STN) � Maximum limit of 300 characters if via a COMMAND FILE (as for general STN) � Maximum limit of 500 characters as a query text file using UPLOAD (page 14), for nucleic acid (/SQN) and translated protein (/TSQN) searches conducted online � Maximum limit of 750 characters as a query text file using UPLOAD, for protein (/SQP) searches conducted online � Maximum limit of 2,000 characters as a query text file using UPLOAD, for BATCH and ALERT searches in all search modes (/SQN, /SQP and /TSQN) � Each line within a query text file using UPLOAD must not exceed 300 characters 1 1 This limit does not apply when using the Sequence Query Upload Wizard in STN Express 8.2 or higher (page 14). GENESEQ on STN (DGENE) Workshop Manual | Page 139
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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
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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
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9590 ANSWERS FOUND ABOVE A THRESHOL
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RUN GETSIM for a SQN BOTH search In
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Upload the sequence and conduct a B
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ADVANCED SIMILARITY SEARCHING In th
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RUN BLAST Advanced similarity searc
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BLAST advanced options Advanced sim
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Altering BLAST parameters Advanced
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Sort the answer set according to si
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9913 ANSWERS FOUND BELOW EXPECTATIO
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Advanced similarity searching L4 AN
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Run a BLAST similarity search with
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Display some records with alignment
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Protein sequences: switching off th
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Sort similarity score descending An
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Upload the sequence query text file
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Review the answers using IDENT and
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RUN GETSIM using the translated (/T
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. . . . Advanced similarity searchi
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Batch Search Mode Advanced similari
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Collection of Batch Results Advance
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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
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: VIII: BLAST advanced options Parame
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note - FIZ Karlsruhe

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