BNFO 240. Usman Roshan. Last time. Traceback for alignment How to select the gap penalties? Benchmark alignments Structural superimposition BAliBASE. Database searching. Suppose we have a set of 1,000,000 sequences
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Introduced the idea of searching for k-mers
Can be done quickly by preprocessing databaseFASTA
Key idea: search for k-mers (short matchig substrings)
quickly by preprocessing the database.
This key idea can also be used for speeding up pairwise
alignments when doing multiple sequence alignments
The scoring matrix Sab is the ratio of Mab to pb