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LecturesPart06

Tool s goal find sequences from database similar goal

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Unformatted text preview: or higher or BLAST (Basic Local Alignment Search Tool) s Goal: find sequences from database similar Goal: to query sequence to s Previous tools use either Previous x direct, theoretically sound but computationally direct, slow approach to examine all possible alignments of query with database (dynamic programming) programming) x indirect, heuristic but computationally fast indirect, approach to find similar sequences by first finding identical stretches (FASTP, FASTA) finding BLAST (Basic Local Alignment Search Tool) s BLAST combines best of both by using BLAST theoretically sound method which searches for similar sequences directly but computationally fast computationally s Reference x S. F. Altschul, W. Gish, W. Miller, E. W. S. Myers and D. J. Lipman. Basic Local D. Alignment Search Tool. J. Mol. Biol. 215:403J. 410 (1990) BLAST basics s Need similarity measure, as in dynamic Need programming - use PAM-120 for proteins programming s Define maximal segment pair (MSP) to be Define the highest scoring pair of identical length segments chosen from 2 sequences (in FASTA terms, highest init1 diagonal) FASTA BLAST basics s Define a segment pair to be locally maximal Define if its score cannot be improved either by extending or by shortening both segments extending BLAST basics s Approach: find segment pairs by first Approach: finding word...
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