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BLAST addendum

BLAST addendum. Sushmita Roy BMI/CS 576. How does BLAST scan the database?. Two indices Preprocess to divide the database into words Query word list. NP NS NT NW NY. MF NY T…. NP GAT…. QECFT…. Database sequence. At Query time.

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BLAST addendum

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  1. BLAST addendum Sushmita Roy BMI/CS 576

  2. How does BLAST scan the database? • Two indices • Preprocess to divide the database into words • Query word list NP NS NT NW NY MFNYT… NPGAT… QECFT… Database sequence

  3. At Query time Step 2: determine all words that score at least T when compared to a word in the query sequence QLQL=9 LNLN=10 NFNF=12, NY=9 … SA none ... NP NS NT NW NY QLNFSAGW MFNYT… NPGAT… QECFT… Database sequence

  4. Some notes • Not clear exactly how the indices are implemented • Not clear whether the first version of BLAST had any pre-processing for the database sequences

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