Download Basic Local Alignment Search Tools Given query (DNA or Protein)

BLAST
http://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
8.1
Global Alignment

Words explain (see O’Reilly BLAST)
 Align ‘coelacanth’ and ‘pelican’
 Score +1 for match, -1 for mismatch, -1 gap
coelacanth
p-elican-
coelacanth
-pelican--
What are scores of these matches? What’s the
best score? Needleman-Wunsch algorithm
Genome Revolution: COMPSCI 004G
8.2
Global Alignment
0
P
-1
E
-2
L
-3
I
-4
C
-5
A
-6
N
-7
C
O
E
L
A
C
A
N
T
H
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-1
-2
Genome Revolution: COMPSCI 004G
-2
-2
-1
0
8.3
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
8.4
Local Alignment
P
0
E
0
L
0
I
0
C
0
A
0
N
0
C
O
E
L
A
C
A
N
T
H
0
0
0
0
0
0
0
0
0
0
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1
2
1
1
4
8.5
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
8.6
BLOSUM 62 scoring matrix

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=sef.figgrp.194
Genome Revolution: COMPSCI 004G
8.7