FASTA

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

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