1. Genome Revolution: COMPSCI 004G 8.1 BLAST http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html l What is BLAST? What is it good for?  Basic Local Alignment Search Tools  Given query (DNA or Protein) find “matches”  What is a match? How do judge a good one? l Two kinds of alignment or matches  Global alignment (sequence to sequence)  Local alignment (subseq to subseq)

2. Genome Revolution: COMPSCI 004G 8.2 Global Alignment l Words explain (see O’Reilly BLAST)  Align ‘coelacanth’ and ‘pelican’  Score +1 for match, -1 for mismatch, -1 gap coelacanth p-elican-- -pelican--  What are scores of these matches? What’s the best score? Needleman-Wunsch algorithm

3. Genome Revolution: COMPSCI 004G 8.3 Global Alignment 0-2-3-4-5-6-7-8-9-10 -2 -3-2 -4 -5 -6 -70 COELACANTH P E L I C A N

4. Genome Revolution: COMPSCI 004G 8.4 Local Alignment l Subsequence alignment rather than global  Advantages? Tradeoffs?  Score +1 for match, -1 for mismatch, -1 gap (co)ELECAN(th) (p)ELICAN  Smith-Waterman: initialize to zero, only score positive, trace-back from highest score

5. Genome Revolution: COMPSCI 004G 8.5 Local Alignment 0000000000 0 01 021 01 0 0 04 COELACANTH P E L I C A N

6. Genome Revolution: COMPSCI 004G 8.6 Analysis l How long does this algorithm take to execute?  How do we measure the complexity/size?  Time v. Memory  l We need a different measure of “gap match” and mismatch?  Just using +1 or -1 doesn’t provide domain specific analysis  In practice use scoring matrix, see ncbi site

7. Genome Revolution: COMPSCI 004G 8.7 BLOSUM 62 scoring matrix l http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=sef.figgrp.194 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=sef.figgrp.194