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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K. Rosario, S. Duffy, and M. Breitbart Diverse circovirus-like genome architectures revealed by environmental metagenomics J. Gen. Virol., October 1, 2009; 90(10): 2418 - 2424. [Abstract] [Full Text] [PDF]
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M. Schmitt and M. Pawlita High-throughput detection and multiplex identification of cell contaminations Nucleic Acids Res., October 1, 2009; 37(18): e119 - e119. [Abstract] [Full Text] [PDF]
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N. Parkinson, D. Stead, J. Bew, J. Heeney, L. Tsror (Lahkim), and J. Elphinstone Dickeya species relatedness and clade structure determined by comparison of recA sequences Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2388 - 2393. [Abstract] [Full Text] [PDF]
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E. Beaumont, D. Vendrame, B. Verrier, E. Roch, F. Biron, F. Barin, F. Mammano, and D. Brand Matrix and Envelope Coevolution Revealed in a Patient Monitored since Primary Infection with Human Immunodeficiency Virus Type 1 J. Virol., October 1, 2009; 83(19): 9875 - 9889. [Abstract] [Full Text] [PDF]
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Y. Jeon, J. M. Kim, J. H. Park, S. H. Lee, C.-N. Seong, S.-S. Lee, and C. O. Jeon Pedobacter oryzae sp. nov., isolated from rice paddy soil Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2491 - 2495. [Abstract] [Full Text] [PDF]
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C.-Y. Wang, C.-C. Ng, W.-S. Tzeng, and Y.-T. Shyu Marinobacter szutsaonensis sp. nov., isolated from a solar saltern Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2605 - 2609. [Abstract] [Full Text] [PDF]
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Y. Zhao, W. Wei, I.-M. Lee, J. Shao, X. Suo, and R. E. Davis Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII) Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2582 - 2593. [Abstract] [Full Text] [PDF]
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R. Manorama, P. K. Pindi, G. S. N. Reddy, and S. Shivaji Bhargavaea cecembensis gen. nov., sp. nov., isolated from the Chagos-Laccadive ridge system in the Indian Ocean Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2618 - 2623. [Abstract] [Full Text] [PDF]
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H. Nakayama-Imaohji, H. Hirakawa, M. Ichimura, S. Wakimoto, S. Kuhara, T. Hayashi, and T. Kuwahara Identification of the Site-Specific DNA Invertase Responsible for the Phase Variation of SusC/SusD Family Outer Membrane Proteins in Bacteroides fragilis J. Bacteriol., October 1, 2009; 191(19): 6003 - 6011. [Abstract] [Full Text] [PDF]
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R. R. Stocsits, H. Letsch, J. Hertel, B. Misof, and P. F. Stadler Accurate and efficient reconstruction of deep phylogenies from structured RNAs Nucleic Acids Res., October 1, 2009; 37(18): 6184 - 6193. [Abstract] [Full Text] [PDF]
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 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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W. Jaratlerdsiri, C. J. Rodriguez-Zarate, S. R. Isberg, C. S. Damayanti, L. G. Miles, N. Chansue, C. Moran, L. Melville, and J. Gongora Distribution of Endogenous Retroviruses in Crocodilians J. Virol., October 1, 2009; 83(19): 10305 - 10308. [Abstract] [Full Text] [PDF]
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M. Naum, E. W. Brown, and R. J. Mason-Gamer Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens Microbiology, October 1, 2009; 155(10): 3187 - 3199. [Abstract] [Full Text] [PDF]
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K. A. Cranston, B. Hurwitz, D. Ware, L. Stein, and R. A. Wing Species Trees from Highly Incongruent Gene Trees in Rice Syst Biol, October 1, 2009; 58(5): 489 - 500. [Abstract] [Full Text] [PDF]
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 K. M. Hamilton, P. W. Shaw, and D. Morritt Prevalence and seasonality of Hematodinium (Alveolata: Syndinea) in a Scottish crustacean community ICES J. Mar. Sci., October 1, 2009; 66(9): 1837 - 1845. [Abstract] [Full Text] [PDF]
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 M. M Desko, D. A Gross, and J. J Kohler Effects of N-glycosylation on the activity and localization of GlcNAc-6-sulfotransferase 1 Glycobiology, October 1, 2009; 19(10): 1068 - 1077. [Abstract] [Full Text] [PDF]
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 E. R.M. Tillier and R. L. Charlebois The human protein coevolution network Genome Res., October 1, 2009; 19(10): 1861 - 1871. [Abstract] [Full Text] [PDF]
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S.-B. Jang, A.-R. Kwon, W.-S. Son, S. J. Park, and B.-J. Lee Crystal Structure of Hypothetical Protein HP0062 (O24902_HELPY) from Helicobacter pylori at 1.65 A Resolution J. Biochem., October 1, 2009; 146(4): 535 - 540. [Abstract] [Full Text] [PDF]
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B.-C. Lee and D. Kim A new method for revealing correlated mutations under the structural and functional constraints in proteins Bioinformatics, October 1, 2009; 25(19): 2506 - 2513. [Abstract] [Full Text] [PDF]
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C. Kemena and C. Notredame Upcoming challenges for multiple sequence alignment methods in the high-throughput era Bioinformatics, October 1, 2009; 25(19): 2455 - 2465. [Abstract] [Full Text] [PDF]
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 D. Sharma, K. Bastard, L. A. Guethlein, P. J. Norman, N. Yawata, M. Yawata, M. Pando, H. Thananchai, T. Dong, S. Rowland-Jones, et al. Dimorphic Motifs in D0 and D1+D2 Domains of Killer Cell Ig-Like Receptor 3DL1 Combine to Form Receptors with High, Moderate, and No Avidity for the Complex of a Peptide Derived from HIV and HLA-A*2402 J. Immunol., October 1, 2009; 183(7): 4569 - 4582. [Abstract] [Full Text] [PDF]
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A. Moreno-Estrada, K. Tang, M. Sikora, T. Marques-Bonet, F. Casals, A. Navarro, F. Calafell, J. Bertranpetit, M. Stoneking, and E. Bosch Interrogating 11 Fast-Evolving Genes for Signatures of Recent Positive Selection in Worldwide Human Populations Mol. Biol. Evol., October 1, 2009; 26(10): 2285 - 2297. [Abstract] [Full Text] [PDF]
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Y. Suzuki, T. Gojobori, and S. Kumar Methods for Incorporating the Hypermutability of CpG Dinucleotides in Detecting Natural Selection Operating at the Amino Acid Sequence Level Mol. Biol. Evol., October 1, 2009; 26(10): 2275 - 2284. [Abstract] [Full Text] [PDF]
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