Introduction to local alignment algorithms

Topics

• Review of Scenario
• Smith-Waterman algorithm (exhaustive local alignment)
• Word-based local alignment (method used by BLAST)
• Homegrown BlastN
• Special guest seminar

• Scenario (same as yesterday's)
• Notes: Alignment of pairs of sequences
• Program: BlastN
• Data: E. coli K12 genome
• Outside reading (optional): Bill Pearson's Tutorial on protein sequence comparison and protein evolution

• National Center for Biotechnology Information (home of BLAST)
• FastA (U. Virginia implementation)

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