FASTA (REST) REST

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.

FASTA stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison.

Free.

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 http://www.ebi.ac.uk/Tools/webservices/about/webservices and the EMBL-EBI Terms of Use: http://www.ebi.ac.uk/Information/termsofuse.html

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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 (http://www.ebi.ac.uk/citexplore/citationDetails.do?externalId=20439314&dataSource=MED) DOI: 10.1093/nar/gkq313 (http://dx.doi.org/10.1093/nar/gkq313)

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 (http://www.ebi.ac.uk/citexplore/citationDetails.do?externalId=3162770&dataSource=MED) DOI: 10.1073/pnas.85.8.2444 (http://dx.doi.org/10.1073/pnas.85.8.2444)