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.
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Below is a list of all the FASTA's available at the EBI. Please note we also provide a 'Programmatic Access to FASTA'.

General FASTA Programs

Tool	Description
FASTA-Protein	Sequence similarity searching against protein databases using FASTA.
FASTA-Nucleotide	Sequence similarity searching against nucleotide databases using FASTA.

Specialised FASTA Programs

Tool	Description
FASTA-ASD server	Sequence similarity searching against the Alternative Splicing Database using FASTA.
FASTA-LGIC Protein server	Protein sequence similarity searching against the Ligand Gated Ion Channel Database using FASTA.
FASTA-LGIC Nucleotide server	Nucleotide sequence similarity searching against the Ligand Gated Ion Channel Database using FASTA.
FASTA-Proteome server	Completed Proteomes FASTA server.
FASTA-Genome server	Completed Genomes FASTA server.
FASTA-SNP server	European SNP database (HGBASE) FASTA searches
FASTA-WGS server	WGS FASTA server.
SSEARCH	SSEARCH is a full implementation of the Smith-Waterman algorithm with well-validated statistical estimates.
GGSEARCH	GGSEARCH compares a protein or DNA sequence to a sequence database producing global-global alignment (Needleman-Wunsch).
GLSEARCH	GLSEARCH compares a protein or DNA sequence to a sequence database.
PSI-Search	PSI-Search, similar to PSI-Blast, combines the Smith-Waterman search algorithm (SSEARCH) with the PSI-Blast (BLASTPGP) profile construction strategy to find distantly related protein sequences.