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Understanding BLAST Database Scanning in Bioinformatics

Learn how BLAST scans databases efficiently using preprocess techniques and query word list. Understand database sequence processing and scoring mechanism. Explore the evolution of BLAST indices over time.

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Understanding BLAST Database Scanning in Bioinformatics

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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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