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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B. E. Dutilh, M. A. Huynen, and M. Strous Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly Bioinformatics, November 1, 2009; 25(21): 2878 - 2881. [Abstract] [Full Text] [PDF]
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L. Bartoli, P. Fariselli, A. Krogh, and R. Casadio CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information Bioinformatics, November 1, 2009; 25(21): 2757 - 2763. [Abstract] [Full Text] [PDF]
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 S. M. Bowman, A. Piwowar, E. D. Arnone, R. Matsumoto, G. B. Koudelka, and S. J. Free Characterization of GPIT-1 and GPIT-2, two auxiliary components of the Neurospora crassa GPI transamidase complex Mycologia, November 1, 2009; 101(6): 764 - 772. [Abstract] [Full Text] [PDF]
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 K. Yamatoya, K. Yoshida, C. Ito, M. Maekawa, M. Yanagida, K. Takamori, H. Ogawa, Y. Araki, K. Miyado, Y. Toyama, et al. Equatorin: Identification and Characterization of the Epitope of the MN9 Antibody in the Mouse Biol Reprod, November 1, 2009; 81(5): 889 - 897. [Abstract] [Full Text] [PDF]
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 K. Yura, S. Sulaiman, Y. Hatta, M. Shionyu, and M. Go RESOPS: A Database for Analyzing the Correspondence of RNA Editing Sites to Protein Three-Dimensional Structures Plant Cell Physiol., November 1, 2009; 50(11): 1865 - 1873. [Abstract] [Full Text] [PDF]
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R. Carter and G. Drouin The Evolutionary Rates of Eukaryotic RNA Polymerases and of Their Transcription Factors Are Affected by the Level of Concerted Evolution of the Genes They Transcribe Mol. Biol. Evol., November 1, 2009; 26(11): 2515 - 2520. [Abstract] [Full Text] [PDF]
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 C. Pucciariello, G. Innocenti, W. Van de Velde, A. Lambert, J. Hopkins, M. Clement, M. Ponchet, N. Pauly, S. Goormachtig, M. Holsters, et al. (Homo)glutathione Depletion Modulates Host Gene Expression during the Symbiotic Interaction between Medicago truncatula and Sinorhizobium meliloti Plant Physiology, November 1, 2009; 151(3): 1186 - 1196. [Abstract] [Full Text] [PDF]
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P. David, N. W.G. Chen, A. Pedrosa-Harand, V. Thareau, M. Sevignac, S. B. Cannon, D. Debouck, T. Langin, and V. Geffroy A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean Plant Physiology, November 1, 2009; 151(3): 1048 - 1065. [Abstract] [Full Text] [PDF]
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 G. M. Nava, D. Y. Lee, J. H. Ospina, S.-Y. Cai, and H. R. Gaskins Genomic analyses reveal a conserved glutathione homeostasis pathway in the invertebrate chordate Ciona intestinalis Physiol Genomics, November 1, 2009; 39(3): 183 - 194. [Abstract] [Full Text] [PDF]
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 R. Freire, A. Arias, J. Mendez, and A. Insua SEQUENCE VARIATION OF THE INTERNAL TRANSCRIBED SPACER (ITS) REGION OF RIBOSOMAL DNA IN CERASTODERMA SPECIES (BIVALVIA: CARDIIDAE) J. Mollus. Stud., October 30, 2009; (2009) eyp047v1. [Abstract] [Full Text] [PDF]
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K. Richter, S. Brar, M. Ray, P. Pisitkun, S. Bolland, L. Verkoczy, and M. Diaz Speckled-like Pattern in the Germinal Center (SLIP-GC), a Nuclear GTPase Expressed in Activation-induced Deaminase-expressing Lymphomas and Germinal Center B Cells J. Biol. Chem., October 30, 2009; 284(44): 30652 - 30661. [Abstract] [Full Text] [PDF]
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C. J. A. Sigrist, L. Cerutti, E. de Castro, P. S. Langendijk-Genevaux, V. Bulliard, A. Bairoch, and N. Hulo PROSITE, a protein domain database for functional characterization and annotation Nucleic Acids Res., October 25, 2009; (2009) gkp885v1. [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., October 23, 2009; (2009) gkp831v1. [Abstract] [Full Text] [PDF]
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H. Roy and M. Ibba Broad Range Amino Acid Specificity of RNA-dependent Lipid Remodeling by Multiple Peptide Resistance Factors J. Biol. Chem., October 23, 2009; 284(43): 29677 - 29683. [Abstract] [Full Text] [PDF]
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E. Desmond and S. Gribaldo Phylogenomics of Sterol Synthesis: Insights into the Origin, Evolution, and Diversity of a Key Eukaryotic Feature Gen Biol Evol, October 20, 2009; 2009(0): 364 - 381. [Abstract] [Full Text] [PDF]
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A. Oberai, N. H. Joh, F. K. Pettit, and J. U. Bowie Structural imperatives impose diverse evolutionary constraints on helical membrane proteins PNAS, October 20, 2009; 106(42): 17747 - 17750. [Abstract] [Full Text] [PDF]
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J. Chang, F. D. Mast, A. Fagarasanu, D. A. Rachubinski, G. A. Eitzen, J. B. Dacks, and R. A. Rachubinski Pex3 peroxisome biogenesis proteins function in peroxisome inheritance as class V myosin receptors J. Cell Biol., October 19, 2009; 187(2): 233 - 246. [Abstract] [Full Text] [PDF]
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