COPYRIGHT NOTICE
Copyright 1988, 1991, 1992, 1994, 1995, 1996 by William R.
Pearson and the University of Virginia. All rights reserved. The
FASTA program and documentation may not be sold or incorporated
into a commercial product, in whole or in part, without written
consent of William R. Pearson and the University of Virginia.
For further information regarding permission for use or
reproduction, please contact: David Hudson, Assistant Provost for
Research, University of Virginia, P.O. Box 9025, Charlottesville,
VA 22906-9025, (434) 924-6853
The FASTA program package
Introduction
This documentation describes the version 2.0x of the FASTA
program package (see W. R. Pearson and D. J. Lipman (1988),
"Improved Tools for Biological Sequence Analysis", PNAS 85:2444-
2448, and W. R. Pearson (1990) "Rapid and Sensitive Sequence
Comparison with FASTP and FASTA" Methods in Enzymology 183:63-
98). Version 2.0 modifies version 1.8 to include explicit
statistical estimates for similarity scores based on the extreme
value distribution. In addition, FASTA protein alignments now
use the Smith-Waterman algorithm with no limitation on gap size.
FASTA and SSEARCH now use the BLOSUM50 matrix by default, with
options to change gap penalties on the command line. Version 1.7
replaces rdf2 and rss with prdf and prss, which use the extreme-
value distribution to calculate accurate probability estimates.
Although there are a large number of programs in this package,
they belong to four groups:
Library search programs: FASTA, FASTX, TFASTA, TFASTX, SSEARCH
Local homology programs: LFASTA, PLFASTA, LALIGN, PLALIGN, FLALIGN
Statistical significance: PRDF, RELATE, PRSS, RANDSEQ
Global alignment: ALIGN
In addition, I have included several programs for protein
sequence analysis, including a Kyte-Doolittle hydropathicity
plotting program (GREASE, TGREASE), and a secondary structure
prediction package (GARNIER).
The FASTA sequence comparison programs on this disk are
improved versions of the FASTP program, originally described in
