Scribe: D. Slotta

Today's Handouts and Announcements

• None

Today's Topics

• Blast (Basic Local Alignment Search Tool)
  • Algorithm
    1. Determine all w-mers in q. Add all w-mers that score at least T with one of q's w-mers. This is the set of seeds.
    2. Build finite automaton to scan for seeds.
    3. For each seed in S_k, add each occurrence of that seed in q or w-mer in q with a score T. (Extend seeds)

       To add gaps, use dynamic programming for step 3.

  • Blast returns:
    1. Length of longest segment pair.
    2. Probability that this occurred by chance.

  • Statistical Estimate (see references)

Today's Sources

• Setubal and Meidanis: Section 3.5.2.
• Basic Local Alignment Search Tool: Altschul, Gish, Miller, Myers, Lipman
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs: Altschul, Madden, Schaffer, Zhang, Zhang, Miller, Lipman