Sequence Similarity Search - I : Basic Local Alignment Search Tool (BLAST)~ Bioinformatics Made Simple.com

Sequence Similarity Search - I : Basic Local Alignment Search Tool (BLAST)

Basic Local Alignment Search Tool (BLAST) is a bioinformatics Tool to finds regions of local similarity between sequences. BLAST compares biological sequence information, nucleotide or protein sequences, to sequence databases and calculates the statistical significance of matches and thus helps us to infer functional and evolutionary relationships between sequences. Different types of BLASTs are available according to the query sequences. BLAST is actually a family of programs where every member perform specific function

blastp amino acid query Vs a protein sequence database

blastn nucleotide query sequence Vs nucleotide sequence database

blastx nucleotide query sequence translated in all reading frames Vs protein sequence database

tblastn protein query sequence Vs nucleotide sequence database

tblastx six-frame translatied nucleotide query sequence Vs six-frame translations of a nucleotide sequence database

Beside the above mentioned BLAST type some relatively new BLAST algorithms have been developed by different scientific groups to deals efficiently with sequences. Some examples are

Position-Specific Iterative BLAST (PSI-BLAST) - is used to find distant relatives of a protein because of its high sensitivity in picking up distant evolutionary relationships than a standard protein-protein BLAST.

Megablast - for comparision of large numbers of query sequences

Discontiguous megablast - for comparison of large set of diverged sequences

Among these BLAST programs, BLASTn and BLASTp are the most commonly used because they use direct comparisons of sequences.

Further reading :

1. Blast Program Selection Guide HERE

2. Discontiguous Mega BLAST HERE

3. BLAST tutorial HERE

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