Rapid and Sensitive Protein Similarity Searches

DOI Web Site 70 Citations
  • David J. Lipman
    Mathematical Research Branch of the National Institute of Arthritis, Diabetes, and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20205.
  • William R. Pearson
    Department of Biochemistry, University of Virginia, Charlottesville 22908.

Abstract

<jats:p>An algorithm was developed which facilitates the search for similarities between newly determined amino acid sequences and sequences already available in databases. Because of the algorithm's efficiency on many microcomputers, sensitive protein database searches may now become a routine procedure for molecular biologists. The method efficiently identifies regions of similar sequence and then scores the aligned identical and differing residues in those regions by means of an amino acid replaceability matrix. This matrix increases sensitivity by giving high scores to those amino acid replacements which occur frequently in evolution. The algorithm has been implemented in a computer program designed to search protein databases very rapidly. For example, comparison of a 200-amino-acid sequence to the 500,000 residues in the National Biomedical Research Foundation library would take less than 2 minutes on a minicomputer, and less than 10 minutes on a microcomputer (IBM PC).</jats:p>

Journal

  • Science

    Science 227 (4693), 1435-1441, 1985-03-22

    American Association for the Advancement of Science (AAAS)

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