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Advanced similarity searching Amino acid sequences: changing matrices, word size and E-value Search Question: Find similar sequences to: GSSFLSPEHQR Search Strategy To conduct a similarity search for protein sequences with BLAST altering matrix, word size and E-value parameters… Step 1 Run a BLAST similarity search with default settings Step 2 Run a BLAST search with altered settings Step 3 Keep all answers and sort them by similarity score Step 4 Display some records with alignment Step 4 Display selected records in a bibliographic format Page 58 | GENESEQ on STN (DGENE) Workshop Manual
Run a BLAST similarity search with default settings => RUN BLAST GSSFLSPEHQR/SQP BLAST Version 2.2 The BLAST software is used herein with permission of the National Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM). See also, Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402 BLAST SEARCHING . . . . Lambda K H 0.311 0.127 0.369 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 29,048,764 Number of Sequences: 6631376 Number of extensions: 127418 Number of successful extensions: 1295 Number of sequences better than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 1295 Number of HSP's gapped (non-prelim): 0 length of query: 11 length of database: 1,256,955,012 effective HSP length: 0 effective length of query: 24 effective length of database: 1,256,955,012 effective search space: 30166920288 effective search space used: 30166920288 T: 11 A: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 70 (31.6 bits) NO ANSWERS FOUND BELOW EXPECTATION VALUE OF 10.0 Helpful HINT Advanced similarity searching The BLAST summary gives the BLAST parameters. In this example, the default values are used (page 137). These are: c) Matrix: BLOSUM-62 d) Gap penalties: 11 for opening and 1 for extending a gap For this peptide sequence query, no answer sequences are found using the default BLAST settings. NCBI recommended settings 1 for short amino acid sequence queries (
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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 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: Advanced similarity searching L4 AN
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
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Protein SUBSEQUENCE FAMILY Search S
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Nucleic acid EXACT Search Sequence
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Nucleic Acid SUBSEQUENCE Search Seq
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Using variability symbols Sequence
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Excluding residues Sequence Code Ma
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Repeat the search with the compleme
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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
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Nucleic acids Appendices Nucleotide
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Appendices Feature Definition termi
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Search fields VI: DGENE search and
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VII: Variability Symbols for GETSEQ
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VIII: BLAST advanced options Parame
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IX: Sequence Search Query Limits Ap
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