Genome Revolution: COMPSCI 004G 8.1

BLASThttp://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html 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?

Two kinds of alignment or matches Global alignment (sequence to sequence) Local alignment (subseq to subseq)

Genome Revolution: COMPSCI 004G 8.2

Global Alignment Words explain (see O’Reilly BLAST)

Align ‘coelacanth’ and ‘pelican’ Score +1 for match, -1 for mismatch, -1

gap

coelacanth coelacanthp-elican-- -pelican--

What are scores of these matches? What’s the best score? Needleman-Wunsch algorithm

Genome Revolution: COMPSCI 004G 8.3

Global Alignment

0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10

-1 -1 -2

-2

-3 -2 -2 -1

-4

-5

-6

-7 0

C O E L A C A N T H

PELICAN

Genome Revolution: COMPSCI 004G 8.4

Local Alignment 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

Genome Revolution: COMPSCI 004G 8.5

Local Alignment

0 0 0 0 0 0 0 0 0 000 10 2 10 1000 4

C O E L A C A N T H

PELICAN

Genome Revolution: COMPSCI 004G 8.6

Analysis How long does this algorithm take to

execute? How do we measure the complexity/size? Time v. Memory

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

Genome Revolution: COMPSCI 004G 8.7

BLOSUM 62 scoring matrix http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=sef.figgrp.194