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Nucleic Acids Research, Vol 25, Issue 17 3389-3402, Copyright © 1997 by Oxford University Press


REVIEWS

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

SF Altschul, TL Madden, AA Schaffer, J Zhang, Z Zhang, W Miller and DJ Lipman
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. altschul@ncbi.nlm.nih.gov

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.
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J. Gen. Virol., October 1, 2009; 90(10): 2525 - 2535.
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J. Gen. Virol.Home page
R. A. Valverde and S. Sabanadzovic
A novel plant virus with unique properties infecting Japanese holly fern
J. Gen. Virol., October 1, 2009; 90(10): 2542 - 2549.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
A. S. Lamm, A. Khare, P. Conville, P. C. K. Lau, H. Bergeron, and J. P. N. Rosazza
Nocardia iowensis sp. nov., an organism rich in biocatalytically important enzymes and nitric oxide synthase
Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2408 - 2414.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
N. Vaisman and A. Oren
Salisaeta longa gen. nov., sp. nov., a red, halophilic member of the Bacteroidetes
Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2571 - 2574.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
J. Xiao, Y. Wang, Y. Luo, S.-J. Xie, J.-S. Ruan, and J. Xu
Streptomyces avicenniae sp. nov., a novel actinomycete isolated from the rhizosphere of the mangrove plant Avicennia mariana
Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2624 - 2628.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
S. Qin, J. Li, H.-H. Chen, G.-Z. Zhao, W.-Y. Zhu, C.-L. Jiang, L.-H. Xu, and W.-J. Li
Isolation, Diversity, and Antimicrobial Activity of Rare Actinobacteria from Medicinal Plants of Tropical Rain Forests in Xishuangbanna, China
Appl. Envir. Microbiol., October 1, 2009; 75(19): 6176 - 6186.
[Abstract] [Full Text] [PDF]


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Antimicrob. Agents Chemother.Home page
B. Czesny, S. Goshu, J. L. Cook, and K. C. Williamson
The Proteasome Inhibitor Epoxomicin Has Potent Plasmodium falciparum Gametocytocidal Activity
Antimicrob. Agents Chemother., October 1, 2009; 53(10): 4080 - 4085.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
Y. Ito, Y. Kawai, K. Arakawa, Y. Honme, T. Sasaki, and T. Saito
Conjugative Plasmid from Lactobacillus gasseri LA39 That Carries Genes for Production of and Immunity to the Circular Bacteriocin Gassericin A
Appl. Envir. Microbiol., October 1, 2009; 75(19): 6340 - 6351.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
J. Boguslawska, J. Zycka-Krzesinska, A. Wilcks, and J. Bardowski
Intra- and Interspecies Conjugal Transfer of Tn916-Like Elements from Lactococcus lactis In Vitro and In Vivo
Appl. Envir. Microbiol., October 1, 2009; 75(19): 6352 - 6360.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
J. Vyas, M. R. Gryk, and M. R. Schiller
VENN, a tool for titrating sequence conservation onto protein structures
Nucleic Acids Res., October 1, 2009; 37(18): e124 - e124.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
R. Schwarz, P. N. Seibel, S. Rahmann, C. Schoen, M. Huenerberg, C. Muller-Reible, T. Dandekar, R. Karchin, J. Schultz, and T. Muller
Detecting species-site dependencies in large multiple sequence alignments
Nucleic Acids Res., October 1, 2009; 37(18): 5959 - 5968.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
P. S. Kourtev, C. H. Nakatsu, and A. Konopka
Inhibition of Nitrate Reduction by Chromium(VI) in Anaerobic Soil Microcosms
Appl. Envir. Microbiol., October 1, 2009; 75(19): 6249 - 6257.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
S. N. Gardner, A. L. Hiddessen, P. L. Williams, C. Hara, M. C. Wagner, and B. W. Colston Jr
Multiplex primer prediction software for divergent targets
Nucleic Acids Res., October 1, 2009; 37(19): 6291 - 6304.
[Abstract] [Full Text] [PDF]


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MicrobiologyHome page
M. Candela, E. Biagi, M. Centanni, S. Turroni, M. Vici, F. Musiani, B. Vitali, S. Bergmann, S. Hammerschmidt, and P. Brigidi
Bifidobacterial enolase, a cell surface receptor for human plasminogen involved in the interaction with the host
Microbiology, October 1, 2009; 155(10): 3294 - 3303.
[Abstract] [Full Text] [PDF]


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Genome ResHome page
C. Liang, L. Mao, D. Ware, and L. Stein
Evidence-based gene predictions in plant genomes
Genome Res., October 1, 2009; 19(10): 1912 - 1923.
[Abstract] [Full Text] [PDF]


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CarcinogenesisHome page
A. Dowejko, R. J. Bauer, U. D.A. Muller-Richter, and T. E. Reichert
The human homolog of the Drosophila headcase protein slows down cell division of head and neck cancer cells
Carcinogenesis, October 1, 2009; 30(10): 1678 - 1685.
[Abstract] [Full Text] [PDF]


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J Exp BotHome page
M. C. Voicu, J. E. K. Cooke, and J. J. Zwiazek
Aquaporin gene expression and apoplastic water flow in bur oak (Quercus macrocarpa) leaves in relation to the light response of leaf hydraulic conductance
J. Exp. Bot., October 1, 2009; 60(14): 4063 - 4075.
[Abstract] [Full Text] [PDF]


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BioinformaticsHome page
K. Forslund and E. L. Sonnhammer
Benchmarking homology detection procedures with low complexity filters
Bioinformatics, October 1, 2009; 25(19): 2500 - 2505.
[Abstract] [Full Text] [PDF]


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GeneticsHome page
J. P. Foxe and S. I. Wright
Signature of Diversifying Selection on Members of the Pentatricopeptide Repeat Protein Family in Arabidopsis lyrata
Genetics, October 1, 2009; 183(2): 663 - 672.
[Abstract] [Full Text] [PDF]


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Mol Biol EvolHome page
D.-D. Wu, G.-D. Wang, D. M Irwin, and Y.-P. Zhang
A Profound Role for the Expansion of Trypsin-Like Serine Protease Family in the Evolution of Hematophagy in Mosquito
Mol. Biol. Evol., October 1, 2009; 26(10): 2333 - 2341.
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Mol Biol EvolHome page
J. Gu and V. J. Hilser
Sequence-Based Analysis of Protein Energy Landscapes Reveals Nonuniform Thermal Adaptation within the Proteome
Mol. Biol. Evol., October 1, 2009; 26(10): 2217 - 2227.
[Abstract] [Full Text] [PDF]


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Mol Biol EvolHome page
E. A. Franzosa and Y. Xia
Structural Determinants of Protein Evolution Are Context-Sensitive at the Residue Level
Mol. Biol. Evol., October 1, 2009; 26(10): 2387 - 2395.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
A. K. Ghosh, N. Chauhan, S. Rajakumari, G. Daum, and R. Rajasekharan
At4g24160, a Soluble Acyl-Coenzyme A-Dependent Lysophosphatidic Acid Acyltransferase
Plant Physiology, October 1, 2009; 151(2): 869 - 881.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
Z. Tao, H. Liu, D. Qiu, Y. Zhou, X. Li, C. Xu, and S. Wang
A Pair of Allelic WRKY Genes Play Opposite Roles in Rice-Bacteria Interactions
Plant Physiology, October 1, 2009; 151(2): 936 - 948.
[Abstract] [Full Text] [PDF]


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Proc R Soc BHome page
A. Bertucci, E. Tambutte, S. Tambutte, D. Allemand, and D. Zoccola
Symbiosis-dependent gene expression in coral-dinoflagellate association: cloning and characterization of a P-type H+-ATPase gene
Proc R Soc B, September 30, 2009; (2009) rspb.2009.1266v1.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
E. van den Born, A. Bekkelund, M. N. Moen, M. V. Omelchenko, A. Klungland, and P. O. Falnes
Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria
Nucleic Acids Res., September 28, 2009; (2009) gkp774v1.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
L. Zhao, H. Dong, C. C. Zhang, L. Kinch, M. Osawa, M. Iacovino, N. V. Grishin, M. Kyba, and L. J.-s. Huang
A JAK2 Interdomain Linker Relays Epo Receptor Engagement Signals to Kinase Activation
J. Biol. Chem., September 25, 2009; 284(39): 26988 - 26998.
[Abstract] [Full Text] [PDF]


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Gen Biol EvolHome page
O. Zhaxybayeva, W. F. Doolittle, R. T. Papke, and J. P. Gogarten
Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus
Gen Biol Evol, September 23, 2009; 2009(0): 325 - 339.
[Abstract] [Full Text] [PDF]



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