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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E. R. Moellering and C. Benning RNA Interference Silencing of a Major Lipid Droplet Protein Affects Lipid Droplet Size in Chlamydomonas reinhardtii Eukaryot. Cell, January 1, 2010; 9(1): 97 - 106. [Abstract] [Full Text] [PDF]
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 J. M. Young, H. F. Massa, L. Hsu, and B. J. Trask Extreme variability among mammalian V1R gene families Genome Res., January 1, 2010; 20(1): 10 - 18. [Abstract] [Full Text] [PDF]
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A. P. Scafaro, P. A. Haynes, and B. J. Atwell Physiological and molecular changes in Oryza meridionalis Ng., a heat-tolerant species of wild rice J. Exp. Bot., January 1, 2010; 61(1): 191 - 202. [Abstract] [Full Text] [PDF]
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 D. J. Thomas, G. M. Nava, S.-Y. Cai, J. L. Boyer, A. Hernandez-Zavala, and H. R. Gaskins Arsenic (+ 3 Oxidation State) Methyltransferase and the Methylation of Arsenicals in the Invertebrate Chordate Ciona intestinalis Toxicol. Sci., January 1, 2010; 113(1): 70 - 76. [Abstract] [Full Text] [PDF]
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R. A. Walker, I. Slapetova, J. Slapeta, C. M. Miller, and N. C. Smith The Glycosylation Pathway of Eimeria tenella Is Upregulated during Gametocyte Development and May Play a Role in Oocyst Wall Formation Eukaryot. Cell, January 1, 2010; 9(1): 127 - 135. [Abstract] [Full Text] [PDF]
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M. Arzanlou, P. W. Crous, and L.-H. Zwiers Evolutionary Dynamics of Mating-Type Loci of Mycosphaerella spp. Occurring on Banana Eukaryot. Cell, January 1, 2010; 9(1): 164 - 172. [Abstract] [Full Text] [PDF]
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 S. Kumar, A. Kumar, and V. K. Dixit Diversity in the cag pathogenicity island of Helicobacter pylori isolates in populations from North and South India J. Med. Microbiol., January 1, 2010; 59(1): 32 - 40. [Abstract] [Full Text] [PDF]
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E. Barsoum, P. Martinez, and S. U. Astrom {alpha}3, a transposable element that promotes host sexual reproduction Genes & Dev., January 1, 2010; 24(1): 33 - 44. [Abstract] [Full Text] [PDF]
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R. L. Stingley, W. Zou, T. M. Heinze, H. Chen, and C. E. Cerniglia Metabolism of azo dyes by human skin microbiota J. Med. Microbiol., January 1, 2010; 59(1): 108 - 114. [Abstract] [Full Text] [PDF]
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E. W. Sayers, T. Barrett, D. A. Benson, E. Bolton, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, S. Federhen, et al. Database resources of the National Center for Biotechnology Information Nucleic Acids Res., January 1, 2010; 38(suppl_1): D5 - D16. [Abstract] [Full Text] [PDF]
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 L. A. Lovasco, K. A. Seymour, K. Zafra, C. W. O'Brien, C. Schorl, and R. N. Freiman Accelerated Ovarian Aging in the Absence of the Transcription Regulator TAF4B in Mice Biol Reprod, January 1, 2010; 82(1): 23 - 34. [Abstract] [Full Text] [PDF]
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 R. M.R. Gawryluk and M. W. Gray An Ancient Fission of Mitochondrial cox1 Mol. Biol. Evol., January 1, 2010; 27(1): 7 - 10. [Abstract] [Full Text] [PDF]
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B. Contreras-Moreira 3D-footprint: a database for the structural analysis of protein-DNA complexes Nucleic Acids Res., January 1, 2010; 38(suppl_1): D91 - D97. [Abstract] [Full Text] [PDF]
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W. Li, H. McWilliam, A. R. de la Torre, A. Grodowski, I. Benediktovich, M. Goujon, S. Nauche, and R. Lopez Non-redundant patent sequence databases with value-added annotations at two levels Nucleic Acids Res., January 1, 2010; 38(suppl_1): D52 - D56. [Abstract] [Full Text] [PDF]
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 D. S. Hekmat-Scafe, A. Mercado, A. A. Fajilan, A. W. Lee, R. Hsu, D. B. Mount, and M. A. Tanouye Seizure Sensitivity Is Ameliorated by Targeted Expression of K+-Cl- Cotransporter Function in the Mushroom Body of the Drosophila Brain Genetics, January 1, 2010; 184(1): 171 - 183. [Abstract] [Full Text] [PDF]
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R. Leinonen, R. Akhtar, E. Birney, J. Bonfield, L. Bower, M. Corbett, Y. Cheng, F. Demiralp, N. Faruque, N. Goodgame, et al. Improvements to services at the European Nucleotide Archive Nucleic Acids Res., January 1, 2010; 38(suppl_1): D39 - D45. [Abstract] [Full Text] [PDF]
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D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and E. W. Sayers GenBank Nucleic Acids Res., January 1, 2010; 38(suppl_1): D46 - D51. [Abstract] [Full Text] [PDF]
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R. Leplae, G. Lima-Mendez, and A. Toussaint ACLAME: A CLAssification of Mobile genetic Elements, update 2010 Nucleic Acids Res., January 1, 2010; 38(suppl_1): D57 - D61. [Abstract] [Full Text] [PDF]
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 L. Montoya, I. Haug, and V.M. Bandala Two Lactarius species associated with a relict Fagus grandifolia var. mexicana population in a Mexican montane cloud forest Mycologia, January 1, 2010; 102(1): 153 - 162. [Abstract] [Full Text] [PDF]
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H. S. Kim, T. Murphy, J. Xia, D. Caragea, Y. Park, R. W. Beeman, M. D. Lorenzen, S. Butcher, J. R. Manak, and S. J. Brown BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum Nucleic Acids Res., January 1, 2010; 38(suppl_1): D437 - D442. [Abstract] [Full Text] [PDF]
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H. R. Ansari, D. R. Flower, and G. P. S. Raghava AntigenDB: an immunoinformatics database of pathogen antigens Nucleic Acids Res., January 1, 2010; 38(suppl_1): D847 - D853. [Abstract] [Full Text] [PDF]
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M. Mihara, T. Itoh, and T. Izawa SALAD database: a motif-based database of protein annotations for plant comparative genomics Nucleic Acids Res., January 1, 2010; 38(suppl_1): D835 - D842. [Abstract] [Full Text] [PDF]
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