UNIT 3.9 Finding Protein and Nucleotide Similarities with FASTA

  1. William Pearson

Published Online: 1 FEB 2004

DOI: 10.1002/0471250953.bi0309s04

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Pearson, W. 2004. Finding Protein and Nucleotide Similarities with FASTA. Current Protocols in Bioinformatics. 8:3.9:3.9.1–3.9.23.

Author Information

  1. University of Virginia School of Medicine, Charlottesville, Virginia

Publication History

  1. Published Online: 1 FEB 2004
  2. Published Print: DEC 2003

This is not the most recent version of the article. View current version (24 MAR 2016)


The FASTA package provides a comprehensive set of similarity searching programs, similar to those provided by the BLAST package, and some additional programs that are not provided by BLAST for searching with short peptides and oligonucleotides. The FASTA programs work with a wide variety of database formats, including mySQL sequence databases. FASTA provides very accurate statistical significance estimates, and is more sensitive than BLASTN when comparing DNA sequences. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons.