Homology

Homology - Accelerating sequence alignment and homology...

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Accelerating sequence alignment and homology search algorithms BioE131/231
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DP Accelerator Hardware
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Faster alignment Smith-Waterman, Gotoh, etc., guarantee the best-scoring alignment However, they are too slow to be practical (except with expensive h/w) Subsequent algorithms attempted to provide approximate solutions FASTA BLAST
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FASTA (1988) Acceleration of the Smith-Waterman algorithm Identify strong diagonals in dotplots Use exact word hits to find these diagonals Rescore best N diagonals with approximate word hits Try to join together good diagonals For sequence-pairs that score well under these criteria, do full SW alignment
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Homology Search: Good alignments have ungapped diagonal runs Such runs contain conserved words BLAST : lookup table of high-scoring words
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BLAST (1990) Basic Local Alignment Search Tool Altschul, Gish, Miller, Myers, Lipman Motivation: FASTA still too slow Idea: find fewer, but better, seed hits Uses longer word sizes Allows approximate word hits in initial search phase
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Homology - Accelerating sequence alignment and homology...

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