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Introduction to similarity searching Nucleic acid sequences <strong>note</strong> For nucleotide similarity searching the GETSIM (FASTA) default is single strand (SIN). In contrast the BLAST default is BOTH strands. In order to run a corresponding GETSIM search BOTH must be specified, e.g. => RUN GETSIM L1 /SQN BOTH Search Question: Find nucleic acid sequences of more than 100 nucleotides which have similarity to the following sequence: Page 36 | GENESEQ on STN (DGENE) Workshop Manual GGGUUUAGGAGUGGUAGGUCUUACGAUGCCAGCUGUAAUG CCUACCGGATAA Search Strategy To conduct a GETSIM search for nucleic acid sequences… Step 1 RUN GETSIM using the SQN BOTH option Step 2 Refine the answer set further by sequence length Step 3 Sort the answer set by similarity score Step 4 Display results with ALIGN and SCORE
RUN GETSIM for a SQN BOTH search Introduction to similarity searching => FILE DGENE Sequence queries can be entered directly on FILE 'DGENE' ENTERED AT 13:06:43 ON 28 DEC 2010 the command line, or sent as a plain text file COPYRIGHT (C) 2010 THOMSON REUTERS via the Query Upload Wizard (page 14). => RUN GETSIM GGGUUUAGGAGUGGUAGGUCUUACGAUGCCAGCUGUAAUGCCUACCGGATAA/SQN BOTH RUN GETSIM AT 13:07:03 ON 28 DEC 2010 COPYRIGHT (C) 2010 <strong>FIZ</strong> KARLSRUHE GMBH . . . . 8725 ANSWERS FOUND ABOVE A THRESHOLD OF 67 QUERY SELF SCORE VALUE IS 260 BEST ANSWER SCORE VALUE IS 260 Similarity The Best Answer Score value is also Score given. In this example, there is at least 260 | one perfect answer match to the query. | | | | | | The graphic representation gives a count | of hit sequences (x-axis) and similarity | score (y-axis). The graph gives a visual | clue about the proportion of similar and 130 | not so similar sequences in the answer set. | | |||| ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| Answer Count 1750 3500 5250 7000 8750 ENTER EITHER THE NUMBER OF ANSWERS YOU WISH TO KEEP OR ENTER MINIMUM PERCENT OF SELF SCORE FOLLOWED BY % (BEST ANSWER PERCENTAGE OF SELF SCORE IS 100%) ENTER (ALL) OR ? :ALL In this example, ALL are answers kept (L1). L1 RUN STATEMENT CREATED L1 8722 GGGUUUAGGAGUGGUAGGUCUUACGAUGCCAGCUGUAAUGCCUACCGGATAA/SQN.BOTH Answer set arranged by accession number; to sort by descending similarity score, enter at an arrow prompt (=>) "sor score d". Further refinement with sequence length => S L1 AND SQL>100 13125023 SQL>100 L2 8554 L1 AND SQL>100 The Query Self Score value is the ideal score for a perfect answer match. For this example we are not interested in sequences under 101 nucleotides. This is accomplished by making use of the sequence length field, i.e. SQL>100. GENESEQ on STN (DGENE) Workshop Manual | Page 37
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 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 35: Display selected answers in a bibli
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 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 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
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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
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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
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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
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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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