Nucleic Acids Research, Vol 25, Issue 17 3389-3402, Copyright © 1997 by Oxford University Press
SF Altschul, TL Madden, AA Schaffer, J Zhang, Z Zhang, W Miller and DJ Lipman
The BLAST programs are widely used tools for searching protein and DNA
databases for sequence similarities. For protein comparisons, a variety of
definitional, algorithmic and statistical refinements described here
permits the execution time of the BLAST programs to be decreased
substantially while enhancing their sensitivity to weak similarities. A new
criterion for triggering the extension of word hits, combined with a new
heuristic for generating gapped alignments, yields a gapped BLAST program
that runs at approximately three times the speed of the original. In
addition, a method is introduced for automatically combining statistically
significant alignments produced by BLAST into a position-specific score
matrix, and searching the database using this matrix. The resulting
Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately
the same speed per iteration as gapped BLAST, but in many cases is much
more sensitive to weak but biologically relevant sequence similarities.
PSI-BLAST is used to uncover several new and interesting members of the
BRCT superfamily.
REVIEWS
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. altschul@ncbi.nlm.nih.gov
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|
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|
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|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
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|
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 |
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|
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|
|
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|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
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|
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|
|
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|
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|
|
|
|
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G. Peter, J. Tornai-Lehoczki, and D. Dlauchy Trichomonascus apis sp. nov., a heterothallic yeast species from honeycomb Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1550 - 1554. [Abstract] [Full Text] [PDF]
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 M. Zimic, M. Pajuelo, D. Rueda, C. Lopez, Y. Arana, Y. Castillo, M. Calderon, S. Rodriguez, P. Sheen, J. M. Vinetz, et al. Utility of a Protein Fraction with Cathepsin L-Like Activity Purified from Cysticercus Fluid of Taenia solium in the Diagnosis of Human Cysticercosis Am J Trop Med Hyg, June 1, 2009; 80(6): 964 - 970. [Abstract] [Full Text] [PDF]
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M. E. Deadman, P. Hermant, M. Engskog, K. Makepeace, E. R. Moxon, E. K. H. Schweda, and D. W. Hood Lex2B, a Phase-Variable Glycosyltransferase, Adds either a Glucose or a Galactose to Haemophilus influenzae Lipopolysaccharide Infect. Immun., June 1, 2009; 77(6): 2376 - 2384. [Abstract] [Full Text] [PDF]
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 M. Gorissen, N. J Bernier, S. B Nabuurs, G. Flik, and M. O Huising Two divergent leptin paralogues in zebrafish (Danio rerio) that originate early in teleostean evolution J. Endocrinol., June 1, 2009; 201(3): 329 - 339. [Abstract] [Full Text] [PDF]
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T. Kitao, T. Miyoshi-Akiyama, and T. Kirikae AAC(6')-Iaf, a Novel Aminoglycoside 6'-N-Acetyltransferase from Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates Antimicrob. Agents Chemother., June 1, 2009; 53(6): 2327 - 2334. [Abstract] [Full Text] [PDF]
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 A. Y. Golovina, P. V. Sergiev, A. V. Golovin, M. V. Serebryakova, I. Demina, V. M. Govorun, and O. A. Dontsova The yfiC gene of E. coli encodes an adenine-N6 methyltransferase that specifically modifies A37 of tRNA1Val(cmo5UAC) RNA, June 1, 2009; 15(6): 1134 - 1141. [Abstract] [Full Text] [PDF]
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 G. Hong, S. Jiang, M. Yu, Y. Yang, F. Li, F. Xue, and Z. Wei The complete nucleotide sequence of the mitochondrial genome of the cabbage butterfly, Artogeia melete (Lepidoptera: Pieridae) Acta Biochim Biophys Sin, June 1, 2009; 41(6): 446 - 455. [Abstract] [Full Text] [PDF]
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Y. Han, J. M. Burnette III, and S. R. Wessler TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences Nucleic Acids Res., June 1, 2009; 37(11): e78 - e78. [Abstract] [Full Text] [PDF]
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C. Hsiao and L. D. Williams A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center Nucleic Acids Res., June 1, 2009; 37(10): 3134 - 3142. [Abstract] [Full Text] [PDF]
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A. R. Wattam, K. P. Williams, E. E. Snyder, N. F. Almeida Jr., M. Shukla, A. W. Dickerman, O. R. Crasta, R. Kenyon, J. Lu, J. M. Shallom, et al. Analysis of Ten Brucella Genomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle J. Bacteriol., June 1, 2009; 191(11): 3569 - 3579. [Abstract] [Full Text] [PDF]
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H. Thompson, K. A. Homer, S. Rao, V. Booth, and A. H. F. Hosie An Orthologue of Bacteroides fragilis NanH Is the Principal Sialidase in Tannerella forsythia J. Bacteriol., June 1, 2009; 191(11): 3623 - 3628. [Abstract] [Full Text] [PDF]
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F. B. Stabell, N. J. Tourasse, and A.-B. Kolsto A conserved 3' extension in unusual group II introns is important for efficient second-step splicing Nucleic Acids Res., June 1, 2009; 37(10): 3202 - 3214. [Abstract] [Full Text] [PDF]
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R. Maitra and M. J. Sadofsky A WW-like module in the RAG1 N-terminal domain contributes to previously unidentified protein-protein interactions Nucleic Acids Res., June 1, 2009; 37(10): 3301 - 3309. [Abstract] [Full Text] [PDF]
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D. C. Bartholomeu, G. C. Cerqueira, A. C. A. Leao, W. D. daRocha, F. S. Pais, C. Macedo, A. Djikeng, S. M. R. Teixeira, and N. M. El-Sayed Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi Nucleic Acids Res., June 1, 2009; 37(10): 3407 - 3417. [Abstract] [Full Text] [PDF]
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J. Beekwilder, D. Marcozzi, S. Vecchi, R. de Vos, P. Janssen, C. Francke, J. van Hylckama Vlieg, and R. D. Hall Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus Appl. Envir. Microbiol., June 1, 2009; 75(11): 3447 - 3454. [Abstract] [Full Text] [PDF]
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S. Lebeer, T. L. A. Verhoeven, G. Francius, G. Schoofs, I. Lambrichts, Y. Dufrene, J. Vanderleyden, and S. C. J. De Keersmaecker Identification of a Gene Cluster for the Biosynthesis of a Long, Galactose-Rich Exopolysaccharide in Lactobacillus rhamnosus GG and Functional Analysis of the Priming Glycosyltransferase Appl. Envir. Microbiol., June 1, 2009; 75(11): 3554 - 3563. [Abstract] [Full Text] [PDF]
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Y. Wang, R. I. Sadreyev, and N. V. Grishin PROCAIN: protein profile comparison with assisting information Nucleic Acids Res., June 1, 2009; 37(11): 3522 - 3530. [Abstract] [Full Text] [PDF]
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D.-M. Kagkli, V. Iliopoulos, V. Stergiou, A. Lazaridou, and G.-J. Nychas Differential Listeria monocytogenes Strain Survival and Growth in Katiki, a Traditional Greek Soft Cheese, at Different Storage Temperatures Appl. Envir. Microbiol., June 1, 2009; 75(11): 3621 - 3626. [Abstract] [Full Text] [PDF]
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