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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

Julie D. Thompson, Desmond G. Higgins+ and Toby J. Gibson*

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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Int. J. Syst. Evol. Microbiol.Home page
Y.-H. Wu, Y.-Q. Shen, X.-W. Xu, C.-S. Wang, A. Oren, and M. Wu
Pseudidiomarina donghaiensis sp. nov. and Pseudidiomarina maritima sp. nov., isolated from the East China Sea
Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1321 - 1325.
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Int. J. Syst. Evol. Microbiol.Home page
P. K. Pindi, K. H. Kishore, G. S. N. Reddy, and S. Shivaji
Description of Leifsonia kafniensis sp. nov. and Leifsonia antarctica sp. nov.
Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1348 - 1352.
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Int. J. Syst. Evol. Microbiol.Home page
L. Collado, I. Cleenwerck, S. Van Trappen, P. De Vos, and M. J. Figueras
Arcobacter mytili sp. nov., an indoxyl acetate-hydrolysis-negative bacterium isolated from mussels
Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1391 - 1396.
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Int. J. Syst. Evol. Microbiol.Home page
D. Wurdemann, B. J. Tindall, R. Pukall, H. Lunsdorf, C. Strompl, T. Namuth, H. Nahrstedt, M. Wos-Oxley, S. Ott, S. Schreiber, et al.
Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn's disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov.
Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1405 - 1415.
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Int. J. Syst. Evol. Microbiol.Home page
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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Int. J. Syst. Evol. Microbiol.Home page
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. Gen. Virol.Home page
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.
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J. Gen. Virol.Home page
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.
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J EndocrinolHome page
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.
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Antimicrob. Agents Chemother.Home page
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.
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Antimicrob. Agents Chemother.Home page
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.
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Infect. Immun.Home page
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.
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J EndocrinolHome page
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.
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J Antimicrob ChemotherHome page
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.
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Nucleic Acids ResHome page
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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J. Virol.Home page
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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J. Bacteriol.Home page
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.
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Nucleic Acids ResHome page
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.
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Nucleic Acids ResHome page
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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Appl. Environ. Microbiol.Home page
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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Appl. Environ. Microbiol.Home page
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.
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GlycobiologyHome page
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.
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Protein Eng Des SelHome page
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.
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Eukaryot CellHome page
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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Genome ResHome page
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.
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BioinformaticsHome page
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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BioinformaticsHome page
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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BioinformaticsHome page
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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Plant Cell PhysiolHome page
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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Biol. Reprod.Home page
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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