European Bioinformatics Institute (EBI)


Submitter / Source:
Hamish McWilliam (2 months ago)

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Documentation URL(s): Hamish McWilliam (2 months ago)

Login to add a documentation URL Description(s): Hamish McWilliam (2 months ago)FASTA (pronounced FAST-Aye) stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison. This program achieves a high level of sensitivity for similarity searching at high speed. This is achieved by performing optimised searches for local alignments using a substitution matrix. The high speed of this program is achieved by using the observed pattern of word hits to identify potential matches before attempting the more time consuming optimised search. The trade-off between speed and sensitivity is controlled by the ktup parameter, which specifies the size of the word. Increasing the ktup decreases the number of background hits. Not every word hit is investigated but instead initially looks for segment’s containing several nearby hits.

Programs from the FASTA suite included in this service:

* FASTA – protein vs. protein database and nucleotide vs. nucleotide database
* FASTX – translated nucleotide vs. protein database
* FASTY – translated nucleotide vs. protein database
* GGSEARCH – protein vs. protein database using global-global alignment (Needleman-Wunsch)
* GLSEARCH – protein vs. protein database using global-local alignment (global in the query and local in the match)
* SSEARCH – protein vs. protein database using local-local alignment (Smith-Waterman)
* TFASTX – protein vs. translated nucleotide database
* TFASTY – protein vs. translated nucleotide database

Fasta Home:

Login to add a description License(s): Hamish McWilliam (2 months ago)EMBL-EBI Terms of Use:

Login to add license info Cost: Hamish McWilliam (2 months ago)Free.

Login to add cost info Usage Conditions: Hamish McWilliam (2 months ago)E-mail supplied for submission must be a valid e-mail address and no more than 25 concurrent jobs should be submitted at any one time, see and the EMBL-EBI Terms of Use:

Login to add usage conditions info Contact Info: Hamish McWilliam (2 months ago)EBI support team:

Login to add contact info Publications: for this service. This can be a URI to the publication and/or a DOI. Hamish McWilliam (2 months ago)Goujon M., McWilliam H., Li W., Valentin F., Squizzato S., Paern J. and Lopez R. (2010)
“A new bioinformatics analysis tools framework at EMBL-EBI.”
Nucleic Acids Res. 38:W695-9
PMID: 20439314 <;=MED>
DOI: 10.1093/nar/gkq313 <>

Hamish McWilliam (2 months ago)Pearson W.R. and Lipman D.J. (1988)
“Improved tools for biological sequence comparison.”
Proc. Natl. Acad. Sci. U.S.A. 85(8):2444-8.
PMID: 3162770 <;=MED>
DOI: 10.1073/pnas.85.8.2444 <>

Login to add publication info Citations: None Login to add a citation