European Bioinformatics Institute (EBI)

United Kingdom

Submitter / Source:
EMBL-EBI Support (about 1 year ago)

Base URL:

WSDL Location: last cached WSDL file)

Documentation URL(s): Rodrigo Lopez (about 1 year ago)

Hamish McWilliam (9 months ago)

Login to add a documentation URL Description(s): Rodrigo Lopez (about 1 year 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 included in this service:

fasta, fastx, fasty, fastf, fasts, ssearch, tfastx and tfasty

Fasta Home:

Hamish McWilliam (2 months ago)Sequence similarity search using the FASTA suite:


  • FASTA – protein vs. protein database and nucleotide vs. nucleotide database


  • FASTX – nucleotide vs. protein database


  • FASTY – nucleotide vs. protein database


  • GGSEARCH – protein vs. protein database using Needleman-Wunsch


  • GLSEARCH – protein vs. protein database using global alignment in the query and local in the match


  • SSEARCH – protein vs. protein database using Smith-Waterman


  • TFASTX – protein vs. nucleotide database


  • TFASTY – protein vs. nucleotide database


Hamish McWilliam (2 months ago)The WSFasta RPC/encoded SOAP service is deprecated, and due to be retired in 2011.

Please use the following services instead:

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: Rodrigo Lopez (9 months ago)

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: Rodrigo Lopez (9 months ago)

Login to add contact info Publications: for this service. This can be a URI to the publication and/or a DOI. Rodrigo Lopez (9 months ago);=19435877

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