Salient characteristics of FASTA are:
- FASTA tries to find patvhes of regional similarity, rather than trying to find the best alignment between your entire query and an entire database sequence.
- Alignments generated with FASTA can contain gaps.
- FASTA is quite fast. You can either run the program locally or send queries to an E-mail server
- FASTA is not guaranteed to find the best alignment between your query and the database; it may miss matches. This is because it uses a strategy which is expected to find most matches, but sacrifices complete sensitivity in order to gain speed.
A substitution matrix is used during all phases of protein searches (BLASTP, BLASTX, TBLASTN)
- FASTA uses a substitution matrix only for the extension phase. This is in contrast to BLAST, which uses a matrix for both phases. To reduce the penalty of using a substitution matrix for only the second phase, set the ktup parameter to a low value (1). However, this will incur a significant speed penalty.
- Two other on-line documents extensively describing the FASTA algorithm have been written by Fredj Tekaia and Geoffrey Barton
- Methods Enzymol 210:575
- Genomics 11:635
- Methods Enzymol 183:63
- PNAS 85:2444
- The original paper describing FASTA.
This document is intended to serve as a guide to using certain bioinformatics
programs. It cannot be guaranteed to be free of errors or completely up-to-date. If you know of errors or other shortcomings of this document, please mail them
to Keith Robison