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Introduction to similarity searching Introduction Similarity Searching Similarity searching is an advanced form of sequence searching and there are several established algorithms 1 available for use in sequence databases. A typical approach is to take a given sequence query and compare it algorithmically with a complete database of sequences using a detailed similarity scoring matrix. Each database record is assigned a score, relative to the query, and those answers exceeding a defined minimum similarity threshold are delivered to the searcher ranked by a similarity or identity score. Sequences which are identical to a similarity search query will have the highest score, i.e. 100% similarity. However, the key benefit of similarity searching is that it will also deliver answers at less than 100% similarity which will often be similar enough to be of interest to the searcher. This includes answers with insertions, deletions and non-matching regions. It is often impossible to achieve this result via the SCM approach. There are two basic options for similarity searching in DGENE. � RUN BLAST – software using the NCBI BLAST algorithm � RUN GETSIM – software based upon the FASTA algorithm NCBI BLAST The RUN BLAST function makes use of the industry-standard BLAST methodology, and is used in DGENE with the permission of the National Center for Biotechnology Information (NCBI). The Basic Local Alignment Search Tool (BLAST) was described by Altschul et al. 2 in 1997. BLAST search modes � Protein similarity (BLASTP) (/SQP) [default] � Nucleic acid similarity (BLASTN) (/SQN) � Translated protein similarity 3 (TBLASTN) (/TSQN) RUN BLAST offers both offline BATCH (page 79) and ALERT (page 83) options. 1 See for example: http://www.ebi.ac.uk/Tools/similarity.html 2 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. See: http://www.ncbi.nlm.nih.gov/pubmed/9254694. 3 A protein query sequence searched against a nucleotide database translated in all three reading frames. Page 12 | GENESEQ on STN (DGENE) Workshop Manual
GETSIM Introduction to similarity searching The RUN GETSIM function is provided in DGENE by <strong>FIZ</strong> <strong>Karlsruhe</strong> as an alternative to NCBI BLAST (previous page). GETSIM is based on the industry standard FASTA methodology, described by Pearson and Lipman 1 in 1988, and incorporates the similarity scoring system devised by Smith and Waterman 2 in 1981. GETSIM offers the same three search modes as BLAST. GETSIM search modes � Protein similarity (/SQP) [default] � Nucleic acid similarity (/SQN) � Translated protein similarity 3 (TSQN) RUN GETSIM offers both offline BATCH (page 79) and ALERT (page 83) options. Helpful HINT GETSIM is slower than BLAST, so using GETSIM in BATCH mode is recommended. In addition, BATCH query limits are higher. See page 79. 1 "Improved tools for biological sequence comparison", William R. Pearson and David J. Lipman, Proc. Natl. Acad. Sci. Vol. 85 pp 2444 - 2448, April 1988. See: http://www.ncbi.nlm.nih.gov/pubmed/3162770. 2 Smith and Waterman, Advances in Applied Mathematics 2:482-489 (1981). 3 A protein query sequence searched against a nucleotide database translated in all three reading frames. GENESEQ on STN (DGENE) Workshop Manual | Page 13
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: INTRODUCTION TO SIMILARITY SEARCHIN
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
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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
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TEXT AND BIBLIOGRAPHIC In this sect
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Additional search indexes Text and
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Sorting answer sets Text and Biblio
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Prepare and save the query Prepare
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341 ANSWERS FOUND BELOW EXPECTATION
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Text and Bibliographic searching Re
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Display selected answers in a prefe
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SEQUENCE CODE MATCH SEARCHING In th
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Sequence Code Match Searching Exact
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Protein EXACT Search GETSEQ search
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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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