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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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J. Biol. Chem. 279, 38555-38562
   Abstract »    Full Text »    PDF »
Sutterella stercoricanis sp. nov., isolated from canine faeces.
H. L. Greetham, M. D. Collins, G. R. Gibson, C. Giffard, E. Falsen, and P. A. Lawson (2004)
Int J Syst Evol Microbiol 54, 1581-1584
   Abstract »    Full Text »    PDF »
The Major Yolk Protein of Sea Urchins Is Endocytosed by a Dynamin-Dependent Mechanism.
J. M. Brooks and G. M. Wessel (2004)
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   Abstract »    Full Text »    PDF »
Anaerotruncus colihominis gen. nov., sp. nov., from human faeces.
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Appl. Envir. Microbiol. 70, 393-403
   Abstract »    Full Text »    PDF »
Dynamic Programming Based Approximation Algorithms for Sequence Alignment with Constraints.
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INFORMS Journal on Computing 16, 441-458
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DDBJ in the stream of various biological data.
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T. Nakagawa and M. Fukui (2003)
Appl. Envir. Microbiol. 69, 7044-7057
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Mastering seeds for genomic size nucleotide BLAST searches.
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Nucleic Acids Res. 31, 6935-6941
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Ntdin, a Tobacco Senescence-Associated Gene, is Involved in Molybdenum Cofactor Biosynthesis.
S. H. Yang, T. Berberich, A. Miyazaki, H. Sano, and T. Kusano (2003)
Plant Cell Physiol. 44, 1037-1044
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M. J. Wolin, T. L. Miller, M. D. Collins, and P. A. Lawson (2003)
Appl. Envir. Microbiol. 69, 6321-6326
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Identification and Biochemical Characterization of Plant Acylamino Acid-Releasing Enzyme.
Y. Yamauchi, Y. Ejiri, Y. Toyoda, and K. Tanaka (2003)
J. Biochem. 134, 251-257
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Expression and Function of Cell Wall-Bound Cationic Peroxidase in Asparagus Somatic Embryogenesis.
H. Takeda, T. Kotake, N. Nakagawa, N. Sakurai, and D. J. Nevins (2003)
Plant Physiology 131, 1765-1774
   Abstract »    Full Text »    PDF »
Small GTPase Rah/Rab34 Is Associated with Membrane Ruffles and Macropinosomes and Promotes Macropinosome Formation.
P. Sun, H. Yamamoto, S. Suetsugu, H. Miki, T. Takenawa, and T. Endo (2003)
J. Biol. Chem. 278, 4063-4071
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DNA Data Bank of Japan (DDBJ) in XML.
S. Miyazaki, H. Sugawara, T. Gojobori, and Y. Tateno (2003)
Nucleic Acids Res. 31, 13-16
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Small GTPase Tc10 and its homologue RhoT induce N-WASP-mediated long process formation and neurite outgrowth.
T. Abe, M. Kato, H. Miki, T. Takenawa, and T. Endo (2003)
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K. I. Swenson, K. E. Winkler, and A. R. Means (2003)
Mol. Biol. Cell 14, 156-172
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Y. Yoshida, Y. Nakano, A. Amano, M. Yoshimura, H. Fukamachi, T. Oho, and T. Koga (2002)
Microbiology 148, 3961-3970
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Low-Molecular-Mass Polypeptide Components of a Photosystem II Preparation from the Thermophilic Cyanobacterium Thermosynechococcus vulcanus.
Y. Kashino, H. Koike, M. Yoshio, H. Egashira, M. Ikeuchi, H. B. Pakrasi, and K. Satoh (2002)
Plant Cell Physiol. 43, 1366-1373
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Y. Okamura, H. Takeyama, and T. Matsunaga (2001)
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C. Liu, S. J. Wilson, C. Kuei, and T. W. Lovenberg (2001)
J. Pharmacol. Exp. Ther. 299, 121-130
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SSAHA: A Fast Search Method for Large DNA Databases.
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Specific Association of Transcripts of tbzF and tbz17, Tobacco Genes Encoding Basic Region Leucine Zipper-Type Transcriptional Activators, with Guard Cells of Senescing Leaves and/or Flowers.
S. H. Yang, T. Berberich, H. Sano, and T. Kusano (2001)
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Prediction of Protein Functional Domains from Sequences Using Artificial Neural Networks.
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Genome Res. 11, 1410-1417
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{beta}-Galactosidases with a lectin-like domain are expressed in strawberry.
L. Trainotti, R. Spinello, A. Piovan, S. Spolaore, and G. Casadoro (2001)
J. Exp. Bot. 52, 1635-1645
   Abstract »    Full Text »    PDF »
Comparison of Flavivirus Universal Primer Pairs and Development of a Rapid, Highly Sensitive Heminested Reverse Transcription-PCR Assay for Detection of Flaviviruses Targeted to a Conserved Region of the NS5 Gene Sequences.
N. Scaramozzino, J.-M. Crance, A. Jouan, D. A. DeBriel, F. Stoll, and D. Garin (2001)
J. Clin. Microbiol. 39, 1922-1927
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PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.
J. Qian, B. Stenger, C. A. Wilson, J. Lin, R. Jansen, S. A. Teichmann, J. Park, W. G. Krebs, H. Yu, V. Alexandrov, et al. (2001)
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S. Schneider, F. Bosse, D. D'Urso, H.-W. Muller, M. W. Sereda, K.-A. Nave, A. Niehaus, T. Kempf, M. Schnolzer, and J. Trotter (2001)
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E. A. Gaucher, M. M. Miyamoto, and S. A. Benner (2001)
PNAS 98, 548-552
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Distinct Differences in Repertoires of Low-Molecular-Mass Secreted Antigens of Mycobacterium avium Complex and Mycobacterium tuberculosis.
I. Olsen, L. J. Reitan, and H. G. Wiker (2000)
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J. Bacteriol. 182, 4153-4157
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J. Bacteriol. 182, 4188-4197
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T. W. Lovenberg, J. Pyati, H. Chang, S. J. Wilson, and M. G. Erlander (2000)
J. Pharmacol. Exp. Ther. 293, 771-778
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R. Jansen and M. Gerstein (2000)
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J. Biol. Chem. 275, 4973-4980
   Abstract »    Full Text »    PDF »
Cloning and Characterization of 1-Deoxy-D-Xylulose 5-Phosphate Synthase from Streptomyces sp. Strain CL190, Which Uses both the Mevalonate and Nonmevalonate Pathways for Isopentenyl Diphosphate Biosynthesis.
T. Kuzuyama, M. Takagi, S. Takahashi, and H. Seto (2000)
J. Bacteriol. 182, 891-897
   Abstract »    Full Text »
Alkyl Hydroperoxide Reductases C and D Are Major Antigens Constitutively Expressed by Mycobacterium avium subsp. paratuberculosis.
I. Olsen, L. J. Reitan, G. Holstad, and H. G. Wiker (2000)
Infect. Immun. 68, 801-808
   Abstract »    Full Text »    PDF »
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
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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
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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
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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
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