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BLAST BNFO 236 Usman Roshan. BLAST Local pairwise alignment heuristic Faster than standard pairwise alignment programs such as SSEARCH, but less sensitive.

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Presentation on theme: "BLAST BNFO 236 Usman Roshan. BLAST Local pairwise alignment heuristic Faster than standard pairwise alignment programs such as SSEARCH, but less sensitive."— Presentation transcript:

1 BLAST BNFO 236 Usman Roshan

2 BLAST Local pairwise alignment heuristic Faster than standard pairwise alignment programs such as SSEARCH, but less sensitive. Online server: http://www.ncbi.nlm.nih.gov/blast http://www.ncbi.nlm.nih.gov/blast

3 BLAST 1.Given a query q and a target sequence, find substrings of length k (k-mers) of score at least t --- also called hits. k is normally 3 to 5 for amino acids and 12 for nucleotides. 2.Extend each hit to a locally maximal segment. Terminate the extension when the reduction in score exceeds a pre- defined threshold 3.Report maximal segments above score S.

4 Finding k-mers quickly Preprocess the database of sequences: – For each sequence in the database store all k-mers in hash- table. – This takes linear time Query sequence: – For each k-mer in the query sequence look up the hash table of the target to see if it exists – Also takes linear time

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