Blast2seq - BLASTA sequences alignment.

BLAST is a service of the National Center for Biotechnology Information (NCBI). A nucleotide or protein sequence sent to the BLAST server is compared against databases at the NCBI and a summary of matches is returned to the user.

The www BLAST server can be accessed through the home page of the NCBI at www.ncbi.nlm.nih.gov. Stand-alone BLAST binaries can be obtained from the NCBI FTP site.

The BLAST family of programs allows all combinations of DNA or protein query sequences with searches against DNA or protein databases:

     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 (both
               strands) against a protein sequence database.

     tblastn   compares  a  protein  query  sequence  against   a
               nucleotide     sequence    database    dynamically
               translated  in  all  six  reading   frames   (both
               strands).

     tblastx   compares the six-frame translations of  a  nucleo-
               tide query sequence against the six-frame transla-
               tions of a nucleotide sequence database.

Version 2.0 of BLAST allows the introduction of gaps (deletions and insertions) into alignments. With a gapped alignment tool, homologous domains do not have to be broken into several segments. Also, the scoring of gapped results tends to be more biologically meaningful than ungapped results.

The programs, blastn and blastp, offer fully gapped alignments. blastx and tblastn have 'in-frame' gapped alignments and use sum statistics to link alignments from different frames. tblastx provides only ungapped alignments.

The sequence sent to the BLAST server should be in FASTA format, described in http://www.ncbi.nlm.nih.gov/BLAST/fasta.html.

A number of databases are also available. They are described in http://www.ncbi.nlm.nih.gov/BLAST/blast_databases.html.

Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.