BLAST - Heuristic Methods for Sequence Database Searching...

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Heuristic Methods for Sequence Database Searching BMI/CS 576 www.biostat.wisc.edu/bmi576/ Mark Craven craven@biostat.wisc.edu Fall 2011 Heuristic alignment motivation too slow for large databases with high query traffic heuristic methods do fast approximation to dynamic programming – FASTA [Pearson & Lipman, 1988] – BLAST [Altschul et al ., 1990; Altschul et al., Nucleic Acids Research 1997] ) ( mn O
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Heuristic alignment motivation consider the task of searching UnitProtKB/Swiss-Prot against a query sequence: – say our query sequence is 362 amino-acids long – most recent release of DB contains 188,719,038 amino acids – finding local alignments via dynamic programming would entail matrix operations many servers handle thousands of such queries a day (NCBI > 500,000) O (10 11 ) Heuristic alignment heuristic algorithm: a problem-solving method which isn’t guaranteed to find the optimal solution, but which is efficient and finds good solutions key heuristics in BLAST – look for seeds of high scoring alignments – use dynamic programming selectively key tradeoff made: sensitivity vs. speed DB in matches t significan # detected matches t significan # y sensitivit =
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Overview of BLAST (Basic Alignment Search Tool) given: query sequence q , word length w , word score threshold
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BLAST - Heuristic Methods for Sequence Database Searching...

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