FASTA

• Local alignments

  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.

  Gapped alignments

  Alignments generated with FASTA can contain gaps.

  Rapid

  FASTA is quite fast. You can either run the program locally or send queries to an E-mail server

  Heuristic

  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.

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  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
  KRobison@nucleus.harvard.edu