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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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A. E. Christie, J. S. Stevens, M. R. Bowers, M. C. Chapline, D. A. Jensen, K. M. Schegg, J. Goldwaser, M. A. Kwiatkowski, T. K. Pleasant Jr, L. Shoenfeld, et al.
Identification of a calcitonin-like diuretic hormone that functions as an intrinsic modulator of the American lobster, Homarus americanus, cardiac neuromuscular system
J. Exp. Biol., January 1, 2010; 213(1): 118 - 127.
[Abstract] [Full Text] [PDF]


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MicrobiologyHome page
Y. Davila-Martinez, A. L. Ramos-Vega, S. Contreras-Martinez, S. Encarnacion, O. Geiger, and I. M. Lopez-Lara
SMc01553 is the sixth acyl carrier protein in Sinorhizobium meliloti 1021
Microbiology, January 1, 2010; 156(1): 230 - 239.
[Abstract] [Full Text] [PDF]


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MicrobiologyHome page
C. Kroger, J. Stolz, and T. M. Fuchs
myo-Inositol transport by Salmonella enterica serovar Typhimurium
Microbiology, January 1, 2010; 156(1): 128 - 138.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
B. Chawla, A. Jhingran, S. Singh, N. Tyagi, M. H. Park, N. Srinivasan, S. C. Roberts, and R. Madhubala
Identification and Characterization of a Novel Deoxyhypusine Synthase in Leishmania donovani
J. Biol. Chem., January 1, 2010; 285(1): 453 - 463.
[Abstract] [Full Text] [PDF]


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Eukaryot CellHome page
W. Li, B. Metin, T. C. White, and J. Heitman
Organization and Evolutionary Trajectory of the Mating Type (MAT) Locus in Dermatophyte and Dimorphic Fungal Pathogens
Eukaryot. Cell, January 1, 2010; 9(1): 46 - 58.
[Abstract] [Full Text] [PDF]


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Eukaryot CellHome page
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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Genome ResHome page
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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ForestryHome page
V. Lygis, I. Vasiliauskaite, J. Stenlid, and R. Vasaitis
Impact of forest fire on occurrence of Heterobasidion annosum s.s. root rot and other wood-inhabiting fungi in roots of Pinus mugo
Forestry, January 1, 2010; 83(1): 83 - 92.
[Abstract] [Full Text] [PDF]


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J Exp BotHome page
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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Toxicol SciHome page
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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Eukaryot CellHome page
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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Eukaryot CellHome page
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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J Med MicrobiolHome page
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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Genes Dev.Home page
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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J Wildl DisHome page
K. Matsumoto, J. A. Cook, H. K. Goethert, and S. R. Telford III
BARTONELLA SP. INFECTION OF VOLES TRAPPED FROM AN INTERIOR ALASKAN SITE WHERE TICKS ARE ABSENT
J. Wildl. Dis., January 1, 2010; 46(1): 173 - 178.
[Abstract] [Full Text] [PDF]


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J Med MicrobiolHome page
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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Nucleic Acids ResHome page
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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Biol. Reprod.Home page
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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Mol Biol EvolHome page
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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Nucleic Acids ResHome page
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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Nucleic Acids ResHome page
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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GeneticsHome page
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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Nucleic Acids ResHome page
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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Nucleic Acids ResHome page
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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Nucleic Acids ResHome page
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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MycologiaHome page
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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Nucleic Acids ResHome page
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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Nucleic Acids ResHome page
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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Nucleic Acids ResHome page
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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