BLAST

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BLAST (the Basic Local Alignment Search Tool) 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 latest stable version is: 2.2.16 (2007-03-25)

BLAST Assembled Genomes

Note: The following are examples of assembled genomes that can be used as BLAST databases. See here for complete list.

  • Human
  • Mouse
  • Rat
  • Arabidopsis thaliana
  • Oryza sativa
  • Bos taurus
  • Danio rerio
  • Drosophila melanogaster
  • Gallus gallus
  • Pan troglodytes
  • Microbes
  • Apis mellifera

Basic BLAST

nucleotide blast 
Search a nucleotide database using a nucleotide query (Algorithms: blastn, megablast, discontiguous megablast)
protein blast 
Search protein database using a protein query (Algorithms: blastp, psi-blast, phi-blast)
blastx 
Search protein database using a translated nucleotide query
tblastn 
Search translated nucleotide database using a protein query
tblastx 
Search translated nucleotide database using a translated nucleotide query

Blast Family of Programs

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 nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

The default matrix for all protein-protein comparisons is BLOSUM62.

Databases available for BLAST search

see: http://www.ncbi.nlm.nih.gov/blast/blast_databases.shtml

Overview of database search programs

Database
Protein DNA
Query Protein ssearch tfasta (translates database)
fasta tfastx3 (translates database, allowing frame-shift gaps)
blastp tblastn (translates database)
PSI-blast (simplified profile search)
DNA fastx3 (translates query, allowing frameshift gaps) ssearch
blastx (translates query) fasta
blastn
tblastx (translates query and database; no gaps)

See also

References

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.

External links