BLAST

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BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases.

Example

Using the original BLAST substitution matrix and the following alignment, calculate the cost:

AAATTCGGCTTCGGGCTTC
AAAGTGGGCTTCGGGTATA

The original BLAST algorithm used the PAM40 matrix for nucleotide sequences. This included a +5 reward for matches, and a -4 penalty for mismatches, which are added.

 A  A  A  T  T  C  G  G  C  T  T  C  G  G  G  C  T  T  C
+5 +5 +5 -4 +5 -4 +5 +5 +5 +5 +5 +5 +5 +5 +5 -4 -4 +5 -4
 A  A  A  G  T  G  G  G  C  T  T  C  G  G  G  T  A  T  A
14 x 5 = 70
5 x -4 = -20 (cost)
70 - 20 = 50

The sequence therefore has a score of 50, at a cost of 20.

Software

See also

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