Difference between revisions of "BLAST"
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'''BLAST''' (the '''''B'''asic '''L'''ocal '''A'''lignment '''S'''earch '''T'''ool'') 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. | '''BLAST''' (the '''''B'''asic '''L'''ocal '''A'''lignment '''S'''earch '''T'''ool'') 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== | ==BLAST Assembled Genomes== | ||
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The default matrix for all protein-protein comparisons is BLOSUM62. | 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== | ==Overview of database search programs== | ||
| Line 69: | Line 74: | ||
*[[formatdb]] | *[[formatdb]] | ||
*[[FASTA format]] | *[[FASTA format]] | ||
| + | |||
| + | ==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== | ||
| + | *[ftp://ftp.ncbi.nih.gov/blast/ Stand-alone BLAST binaries] | ||
[[Category:Bioinformatics]] | [[Category:Bioinformatics]] | ||
Revision as of 02:44, 9 September 2007
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)
Contents
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.
