Algorithms on Sequences
Algorithms on Sequences
Algorithms on Sequences
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E I,J = MAX<br />
Gotoh’s algorithm (2)<br />
S I,J = MAX<br />
S I,J-1 - G B<br />
E I,J-1 - G X<br />
0<br />
E I,J<br />
F I,J<br />
S I-1,J-1 + sub (X I , Y J)<br />
F I,J = MAX<br />
Cost of a substituti<strong>on</strong><br />
S I-1,J - G B<br />
F I-1,J - G X<br />
• DNA <strong>Sequences</strong><br />
One c<strong>on</strong>sider 2 costs :<br />
• cost of a match positive value<br />
• cost of a mismatch negative value<br />
example : BLAST :<br />
default value = +5 and -4<br />
• Proteins<br />
Use a substituti<strong>on</strong> matrix
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