FASTA Algorithm

William R Pearson, University of Virginia, Charlottesville, Virginia, USA

Published online: September 2005

DOI: 10.1038/npg.els.0005255

The FASTA programs search protein and DNA databases for sequences with statistically significant similarity. The programs compare proteins, DNA and short peptides and oligonucleotides, and run on most popular computers.

Keywords: sequence similarity; homology; statistical significance; protein sequence comparison; DNA sequence comparison

 References
    Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ (1990) A basic local alignment search tool. Journal of Molecular Biology 215: 403–410.
    Altschul SF, Madden TL, Schaffer AA, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389–3402.
    Damer CK, Partridge J, Pearson WR and Haystead TAJ (1998) Rapid identification of protein phosphatase 1-binding proteins by mixed peptide sequencing and data base searching: characterization of a novel holoenzymic form of protein phosphatase 1. Journal of Biological Chemistry 273: 24396–24405.
    Henikoff S and Henikoff JG (1992) Amino acid substitutions matrices from protein blocks. Proceedings of the National Academy of Sciences of the United States of America 89: 10915–10919.
    Lipman DJ and Pearson WR (1985) Rapid and sensitive protein similarity searches. Science 227: 1435–1441.
    Mackey AJ, Haystead TAJ and Pearson WR (2002) Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences. Molecular and Cellular Proteomics 1: 139–147.
    Pearson WR (1991) Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith–Waterman and FASTA algorithms. Genomics 11: 635–650.
    Pearson WR and Lipman DJ (1988) Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America 85: 2444–2448.
    Pearson WR, Wood TC, Zhang Z and Miller W (1997) Comparison of DNA sequences with protein sequences. Genomics 46: 24–36.
    Smith TF and Waterman MS (1981) Identification of common molecular subsequences. Journal of Molecular Biology 147: 195–197.
    Wilbur WJ and Lipman DJ (1983) Rapid similarity searches of nucleic acid and protein data banks. Proceedings of the National Academy of Sciences of the United States of America 80: 726–730.
 Further Reading
    Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods in Enzymology 183: 63–98.
    Pearson WR (1996) Effective protein sequence comparison. Methods in Enzymology 266: 227–258.
    Pearson WR (1998) Empirical statistical estimates for sequence similarity searches. Journal of Molecular Biology 276: 71–84.
    book Pearson WR (2000) "Flexible similarity searching with the FASTA3 program package". In: Misener S and Krawetz SA (eds.) Bioinformatics Methods and Protocols, pp. 185–219. Totowa: Humana Press.
 Web Links
    ePath EMBL-EBI European Bioinformatics Institute. FASTA submission form http://www.ebi.ac.uk/fasta33/
    ePath FASTA Programs at the University of Virginia. FASTA server http://fasta.bioch.virginia.edu
    ePath FTP directory at ftp.virginia.edu. Site for downloading current versions of the FASTA programs ftp://ftp.virginia.edu/pub/fasta/

Related Sub-Topics:

Protein Structure | Bioinformatics | Techniques and Tools in Molecular Biology | Computational Molecular Biology
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Article Title: FASTA Algorithm
 
How to Cite close
Pearson, William R(Sep 2005) FASTA Algorithm. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005255]