Description

The blast programs compare a given sequence (of amino acids or nucleotides) with all the sequences of a database using the statistical methods of Karlin and Altschul [Kar Al 90].

There are six blast applications: blastp, blastn, tblastn, blastx, tblastx and blast3 which were implemented at NCBI:

• blastp: compares an amino acid query sequence against a protein sequence database.

• blastn: compares a nucleotide query sequence against a nucleotide sequence database.

• blastx: compares the six-frame conceptual translation products of a nucleotide query sequence against a protein sequence database.

• tblastn: compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames.

• tblastx: compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

• blast3: compares an amino acid query sequence against a protein sequence database and identifies statistically significant three-way sequence alignments in which the component pairwise alignments are statistically insignificant.

What is a six-frame translation? For our purpose it is enough, if we say, that it is the mapping of nucleotide sequences to amino acid sequences in 6 possible ways.

Blast3 exists in version 1.3, but not in 1.4, so we did not parallelize blast3.