Nucleic Acids Research, 1994, Vol. 22, No. 22 4673-4680
© 1994
COMPUTATIONAL BIOLOGY |
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
European Molecular Biolgoy Laboratory Postfach 102209, Meyerhofstrasse 1, D-69012 Heidelberg, Germany
*To whom correspondence should be addressed
Received July 12, 1994. Revised September 23, 1994. Accepted September 23, 1994.
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to downweight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
+Present address: European Bioinformatics Institute, Hinxton Hall, Hinxton, Cambridge CB10 IRQ. UK
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S. Yoshizawa, M. Wada, K. Kita-Tsukamoto, A. Yokota, and K. Kogure Photobacterium aquimaris sp. nov., a luminous marine bacterium isolated from seawater Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1438 - 1442. [Abstract] [Full Text] [PDF]
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Y. Jeon, S.-S. Lee, B. S. Chung, J. M. Kim, J.-W. Bae, S. K. Park, and C. O. Jeon Mucilaginibacter oryzae sp. nov., isolated from soil of a rice paddy Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1451 - 1454. [Abstract] [Full Text] [PDF]
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 J. Fan Open reading frame structure analysis as a novel genotyping tool for hepatitis E virus and the subsequent discovery of an inter-genotype recombinant J. Gen. Virol., June 1, 2009; 90(6): 1353 - 1358. [Abstract] [Full Text] [PDF]
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C. Cowled, G. Palacios, L. Melville, R. Weir, S. Walsh, S. Davis, A. Gubala, W. I. Lipkin, T. Briese, and D. Boyle Genetic and epidemiological characterization of Stretch Lagoon orbivirus, a novel orbivirus isolated from Culex and Aedes mosquitoes in northern Australia J. Gen. Virol., June 1, 2009; 90(6): 1433 - 1439. [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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K. Kosowska-Shick, L. M. Ednie, P. McGhee, and P. C. Appelbaum Comparative Antipneumococcal Activities of Sulopenem and Other Drugs Antimicrob. Agents Chemother., June 1, 2009; 53(6): 2239 - 2247. [Abstract] [Full Text] [PDF]
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P. Leprohon, D. Legare, and M. Ouellette Intracellular Localization of the ABCC Proteins of Leishmania and Their Role in Resistance to Antimonials Antimicrob. Agents Chemother., June 1, 2009; 53(6): 2646 - 2649. [Abstract] [Full Text] [PDF]
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 C. Peigne, P. Bidet, F. Mahjoub-Messai, C. Plainvert, V. Barbe, C. Medigue, E. Frapy, X. Nassif, E. Denamur, E. Bingen, et al. The Plasmid of Escherichia coli Strain S88 (O45:K1:H7) That Causes Neonatal Meningitis Is Closely Related to Avian Pathogenic E. coli Plasmids and Is Associated with High-Level Bacteremia in a Neonatal Rat Meningitis Model Infect. Immun., June 1, 2009; 77(6): 2272 - 2284. [Abstract] [Full Text] [PDF]
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S. Li, Y. Zhang, Y. Liu, X. Huang, W. Huang, D. Lu, P. Zhu, Y. Shi, C. H K Cheng, X. Liu, et al. Structural and functional multiplicity of the kisspeptin/GPR54 system in goldfish (Carassius auratus) J. Endocrinol., June 1, 2009; 201(3): 407 - 418. [Abstract] [Full Text] [PDF]
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 J. M. Rodriguez-Martinez, A. Briales, C. Velasco, M. C. Conejo, L. Martinez-Martinez, and A. Pascual Mutational analysis of quinolone resistance in the plasmid-encoded pentapeptide repeat proteins QnrA, QnrB and QnrS J. Antimicrob. Chemother., June 1, 2009; 63(6): 1128 - 1134. [Abstract] [Full Text] [PDF]
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P. Qiu, V. Sanfiorenzo, S. Curry, Z. Guo, S. Liu, A. Skelton, E. Xia, C. Cullen, R. Ralston, J. Greene, et al. Identification of HCV protease inhibitor resistance mutations by selection pressure-based method Nucleic Acids Res., June 1, 2009; 37(10): e74 - e74. [Abstract] [Full Text] [PDF]
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B. Klempa, D. H. Kruger, B. Auste, M. Stanko, A. Krawczyk, K. F. Nickel, K. Uberla, and A. Stang A Novel Cardiotropic Murine Adenovirus Representing a Distinct Species of Mastadenoviruses J. Virol., June 1, 2009; 83(11): 5749 - 5759. [Abstract] [Full Text] [PDF]
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S. J. Krebs, T. J. Kirn, and R. K. Taylor Genetic Mapping of Secretion and Functional Determinants of the Vibrio cholerae TcpF Colonization Factor J. Bacteriol., June 1, 2009; 191(11): 3665 - 3676. [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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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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H. Shinmoto, K. Taniguchi, T. Ikawa, K. Kawai, and S.-i. Oshima Phenotypic Diversity of Infectious Red Sea Bream Iridovirus Isolates from Cultured Fish in Japan Appl. Envir. Microbiol., June 1, 2009; 75(11): 3535 - 3541. [Abstract] [Full Text] [PDF]
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H. Teramoto, M. Inui, and H. Yukawa Regulation of Expression of Genes Involved in Quinate and Shikimate Utilization in Corynebacterium glutamicum Appl. Envir. Microbiol., June 1, 2009; 75(11): 3461 - 3468. [Abstract] [Full Text] [PDF]
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F. Casals, A. Ferrer-Admetlla, M. Sikora, A. Ramirez-Soriano, T. Marques-Bonet, S. Despiau, F. Roubinet, F. Calafell, J. Bertranpetit, and A. Blancher Human pseudogenes of the ABO family show a complex evolutionary dynamics and loss of function Glycobiology, June 1, 2009; 19(6): 583 - 591. [Abstract] [Full Text] [PDF]
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S. H. Soror, R. Rao, and J. Cullum Mining the genome sequence for novel enzyme activity: characterisation of an unusual member of the hormone-sensitive lipase family of esterases from the genome of Streptomyces coelicolor A3 (2) Protein Eng. Des. Sel., June 1, 2009; 22(6): 333 - 339. [Abstract] [Full Text] [PDF]
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 P. Masson, D. Lundin, F. Soderbom, and P. Young Characterization of a REG/PA28 Proteasome Activator Homolog in Dictyostelium discoideum Indicates that the Ubiquitin- and ATP-Independent REG{gamma} Proteasome Is an Ancient Nuclear Protease Eukaryot. Cell, June 1, 2009; 8(6): 844 - 851. [Abstract] [Full Text] [PDF]
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X. Wang, H. Tang, J. E. Bowers, and A. H. Paterson Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization Genome Res., June 1, 2009; 19(6): 1026 - 1032. [Abstract] [Full Text] [PDF]
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P. J. A. Cock, T. Antao, J. T. Chang, B. A. Chapman, C. J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics Bioinformatics, June 1, 2009; 25(11): 1422 - 1423. [Abstract] [Full Text] [PDF]
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T. Koressaar, K. Joers, and M. Remm Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms Bioinformatics, June 1, 2009; 25(11): 1349 - 1355. [Abstract] [Full Text] [PDF]
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X. Xia, S. Zhang, Y. Su, and Z. Sun MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields Bioinformatics, June 1, 2009; 25(11): 1433 - 1434. [Abstract] [Full Text] [PDF]
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 Y. Kazama, M. T. Fujiwara, A. Koizumi, K. Nishihara, R. Nishiyama, E. Kifune, T. Abe, and S. Kawano A SUPERMAN-like Gene is Exclusively Expressed in Female Flowers of the Dioecious Plant Silene latifolia Plant Cell Physiol., June 1, 2009; 50(6): 1127 - 1141. [Abstract] [Full Text] [PDF]
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 X. Liu, P. Zhu, K. W.Y. Sham, J. M.L. Yuen, C. Xie, Y. Zhang, Y. Liu, S. Li, X. Huang, C. H.K. Cheng, et al. Identification of a Membrane Estrogen Receptor in Zebrafish with Homology to Mammalian GPER and Its High Expression in Early Germ Cells of the Testis Biol Reprod, June 1, 2009; 80(6): 1253 - 1261. [Abstract] [Full Text] [PDF]
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