note - FIZ Karlsruhe

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Advanced similarity searching Some empty answer sets => RUN ALERT Enter "R" to process alert results or "Q" to process alert queries or alert id to retrieve results or enter . for (end) ALERT REQUEST:R CURRENT RESULTS AVAILABLE NAME RUN DATE 1) AQUAP1 20100319 (No answers - getsim) 2) AQUAP2 20100319 (blast) 3) TAENIA1 20100319 (No answers - getsim) 4) TAENIA2 20100319 (No answers - getsim) ----------------------------- Enter No. of result to be selected or "-" before No. to delete result or "Q" to process alert queries or enter . for (end) RESULT REQUEST:1 NO ANSWERS FOUND ABOVE A THRESHOLD OF 303 QUERY SELF SCORE VALUE IS 7210 CURRENT RESULTS AVAILABLE NAME RUN DATE 1) AQUAP1 20100319 (No answers - getsim) 2) AQUAP2 20100319 (blast) 3) TAENIA1 20100319 (No answers - getsim) 4) TAENIA2 20100319 (No answers - getsim) ----------------------------- Enter No. of result to be selected or "-" before No. to delete result or "Q" to process alert queries or enter . for (end) RESULT REQUEST:END Page 86 | GENESEQ on STN (DGENE) Workshop Manual
TEXT AND BIBLIOGRAPHIC In this section, you will learn SEARCHING � The Basic Index and other text search fields � Publication, application and priority details � Refining BLAST searches with text or date terms
Page 1 and 2:
GENESEQ TM STN ® WORKSHOP MANUAL
Page 3 and 4:
Contents DATABASE CONTENT .........
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 19 and 20:
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 31 and 32:
Display selected answers in a bibli
Page 33 and 34:
9590 ANSWERS FOUND ABOVE A THRESHOL
Page 35 and 36: Display selected answers in a bibli
Page 37 and 38: RUN GETSIM for a SQN BOTH search In
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 69 and 70: Upload the sequence query text file
Page 71 and 72: Review the answers using IDENT and
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: CURRENT RESULTS AVAILABLE NAME RUN
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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