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Science 22 March 1985:
Vol. 227. no. 4693, pp. 1435 - 1441
DOI: 10.1126/science.2983426
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Articles

Science, Vol 227, Issue 4693, 1435-1441
Copyright © 1985 by American Association for the Advancement of Science

articles

Rapid and sensitive protein similarity searches

DJ Lipman and WR Pearson

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 replacability 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).


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I. Olsen, L. J. Reitan, G. Holstad, and H. G. Wiker (2000)
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Cryptochrome Nucleocytoplasmic Distribution and Gene Expression Are Regulated by Light Quality in the Fern Adiantum capillus-veneris.
T. Imaizumi, T. Kanegae, and M. Wada (2000)
PLANT CELL 12, 81-96
   Abstract »    Full Text »    PDF »
Sequences and evolutionary analyses of eukaryotic-type protein kinases from Streptomyces coelicolor A3(2).
H. Ogawara, N. Aoyagi, M. Watanabe, and H. Urabe (1999)
Microbiology 145, 3343-3352
   Abstract »    Full Text »    PDF »
Comparative Genomics of Streptococcus thermophilus Phage Species Supports a Modular Evolution Theory.
S. Lucchini, F. Desiere, and H. Brussow (1999)
J. Virol. 73, 8647-8656
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Identification of a CD4 Domain Required for Interleukin-16 Binding and Lymphocyte Activation.
Y. Liu, W. W. Cruikshank, T. O'Loughlin, P. O'Reilly, D. M. Center, and H. Kornfeld (1999)
J. Biol. Chem. 274, 23387-23395
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The aroC Gene of Aspergillus nidulans Codes for a Monofunctional, Allosterically Regulated Chorismate Mutase.
S. Krappmann, K. Helmstaedt, T. Gerstberger, S. Eckert, B. Hoffmann, M. Hoppert, G. Schnappauf, and G. H. Braus (1999)
J. Biol. Chem. 274, 22275-22282
   Abstract »    Full Text »    PDF »
Fission Yeast Pob1p, Which Is Homologous to Budding Yeast Boi Proteins and Exhibits Subcellular Localization Close to Actin Patches, Is Essential for Cell Elongation and Separation.
M. Toya, Y. Iino, and M. Yamamoto (1999)
Mol. Biol. Cell 10, 2745-2757
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Structure and Evolution of the Alternatively Spliced Fast Troponin T Isoform Gene.
E. A. Bucher, G. K. Dhoot, M. M. Emerson, M. Ober, and C. P. Emerson Jr. (1999)
J. Biol. Chem. 274, 17661-17670
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Prophenoloxidase-activating Enzyme of the Silkworm, Bombyx mori. PURIFICATION, CHARACTERIZATION, AND cDNA CLONING.
D. Satoh, A. Horii, M. Ochiai, and M. Ashida (1999)
J. Biol. Chem. 274, 7441-7453
   Abstract »    Full Text »    PDF »
Purification, Characterization, and Cloning of a Eubacterial 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase, a Key Enzyme Involved in Biosynthesis of Terpenoids.
S. Takahashi, T. Kuzuyama, and H. Seto (1999)
J. Bacteriol. 181, 1256-1263
   Abstract »    Full Text »
DNA-interacting Proteins in the Spermiogenesis of the Mollusc Murex brandaris.
C. Caceres, P. Gimenez-Bonafe, E. Ribes, D. Wouters-Tyrou, A. Martinage, M. Kouach, P. Sautiere, S. Muller, J. Palau, J. A. Subirana, et al. (1999)
J. Biol. Chem. 274, 649-656
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