BLAST
From Bioinformatics.Org Wiki
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
- Blixem - an interactive browser of pairwise BLAST matches that have been stacked up in a "master-slave" multiple alignment
- DBWatcher - a program handling periodic BLAST searches to find similarities to your own sequences
- mpiBLAST - a parallel implementation of NCBI-BLAST that uses database segmentation
- MSPcrunch - a BLAST enhancement filter
- NCBI-BLAST - a US NCBI implementation
- WU-BLAST - a Washington U. implementation
- UGENE - a free BLAST requests scheduler. Supports requests to blastn, blastp and CDD databases located on NCBI server
