May 26, 2018

Collection of programs for searching DNA and protein databases

Version 3 of the FASTA packages contains many programs for searching DNA and protein databases and one program prss3 for evaluating statistical significance from randomly shuffled sequences. Several additional analysis programs, including programs that produce local alignments, are available as part of version 2 of the FASTA package, which is available as the port biology/fasta.

FASTA is described in W. R. Pearson and D. J. Lipman 1988, “Improved Tools for Biological Sequence Analysis”, PNAS 852444-2448; W. R. Pearson 1996 “Effective protein sequence comparison” Meth. Enzymol. 266227-258; Pearson et. al. 1997 Genomics 4624-36; Pearson, 1999 Meth. in Molecular Biology 132185-219.

The FASTA3 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product.

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