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'''FASTA''' is a [[DNA sequence]] alignment and search software package that was first introduced by [[David J. Lipman]] and [[William R. Pearson]] in 1985. The name 'FASTA' is derived from the [[FASTP]] program for protein sequence alignment, and it stands for 'FAST-All', indicating its utility for a wide range of applications.

== History ==

The FASTA software package was developed in the mid-1980s as a method for [[DNA sequence alignment]]. It was designed to be faster than the existing methods at the time, which were often too slow for practical use on the large [[genomic databases]] that were beginning to be developed.

== Functionality ==

FASTA includes a suite of programs for aligning [[nucleotide]] or [[protein]] sequences and searching sequence databases. It uses a heuristic method to find regions of local similarity between sequences, which can then be used to identify regions of potential homology.

The main function of FASTA is to compare a query sequence against a database of sequences, and to identify database sequences that are similar to the query sequence. It can also align two sequences, identify regions of similarity between them, and generate a score that reflects the degree of similarity.

== Algorithm ==

The FASTA algorithm works by first identifying short sequences of exact matches between the query sequence and the database sequences. These short sequences, known as 'k-tuples', are then used as seeds to initiate searches for longer alignments.

The algorithm then extends these initial alignments in both directions, in a process known as 'extension'. This is done by comparing the sequences one base or amino acid at a time, and adding to the alignment score for each match.

Once the extension process is complete, the algorithm calculates a final score for the alignment. This score is based on the number of matches and mismatches in the alignment, as well as the lengths of any gaps.

== Applications ==

FASTA is widely used in [[bioinformatics]] for sequence alignment and database search tasks. It is particularly useful for comparing protein sequences, but can also be used for nucleotide sequences.

FASTA is also often used in [[genomics]] research, for tasks such as identifying genes in a newly sequenced genome, or comparing genomes to identify regions of similarity and difference.

== See also ==

* [[Sequence alignment]]
* [[BLAST]]
* [[Smith-Waterman algorithm]]

== References ==

<references />

[[Category:Bioinformatics software]]
[[Category:Computational biology]]
[[Category:DNA sequencing]]
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FASTA - Revision history

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