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
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  Y. Yogo, S. Zhong, Y. Xu, M. Zhu, Y. Chao, C. Sugimoto, H. Ikegaya, A. Shibuya, and T. Kitamura Conserved archetypal configuration of the transcriptional control region during the course of BK polyomavirus evolution J. Gen. Virol., August 1, 2008; 89(8): 1849 - 1856. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Germain, B. Croise, and S. Valas Field evaluation of a gag/env heteroduplex mobility assay for genetic subtyping of small-ruminant lentiviruses J. Gen. Virol., August 1, 2008; 89(8): 2020 - 2028. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. S. Marengo and D. A. Wassarman A DNA damage signal activates and derepresses exon inclusion in Drosophila TAF1 alternative splicing RNA, August 1, 2008; 14(8): 1681 - 1695. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Li, L. V. Thomassen, A. Majid, B. J. McMahon, D. Bruden, S. McArdle, N. Bano, M. Chung, R. L. Carithers, J. D. Perkins, et al. Investigation of Putative Multisubtype Hepatitis C Virus Infections In Vivo by Heteroduplex Mobility Analysis of Core/Envelope Subgenomes J. Virol., August 1, 2008; 82(15): 7524 - 7532. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J. H. Moonen, N. M. Kamerbeek, A. H. Westphal, S. A. Boeren, D. B. Janssen, M. W. Fraaije, and W. J. H. van Berkel Elucidation of the 4-Hydroxyacetophenone Catabolic Pathway in Pseudomonas fluorescens ACB J. Bacteriol., August 1, 2008; 190(15): 5190 - 5198. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. H. Moonen, S. A. Synowsky, W. A. M. van den Berg, A. H. Westphal, A. J. R. Heck, R. H. H. van den Heuvel, M. W. Fraaije, and W. J. H. van Berkel Hydroquinone Dioxygenase from Pseudomonas fluorescens ACB: a Novel Member of the Family of Nonheme-Iron(II)-Dependent Dioxygenases J. Bacteriol., August 1, 2008; 190(15): 5199 - 5209. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Lommel, T. Willer, and S. Strahl POMT2, a key enzyme in Walker-Warburg syndrome: somatic sPOMT2, but not testis-specific tPOMT2, is crucial for mannosyltransferase activity in vivo Glycobiology, August 1, 2008; 18(8): 615 - 625. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Deshpande, M. R Wilkins, N. Packer, and H. Nevalainen Protein glycosylation pathways in filamentous fungi Glycobiology, August 1, 2008; 18(8): 626 - 637. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Oezguen, S. Kumar, A. Hindupur, W. Braun, B. K. Muralidhara, and J. R. Halpert Identification and Analysis of Conserved Sequence Motifs in Cytochrome P450 Family 2: FUNCTIONAL AND STRUCTURAL ROLE OF A MOTIF 187RFDYKD192 IN CYP2B ENZYMES J. Biol. Chem., August 1, 2008; 283(31): 21808 - 21816. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Pre, V. Caillet, J. Sobilo, and J. McCarthy Characterization and Expression Analysis of Genes Directing Galactomannan Synthesis in Coffee Ann. Bot., August 1, 2008; 102(2): 207 - 220. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. M. Reijns, R. D. Alexander, M. P. Spiller, and J. D. Beggs A role for Q/N-rich aggregation-prone regions in P-body localization J. Cell Sci., August 1, 2008; 121(15): 2463 - 2472. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. G. Hall How Well Does the HoT Score Reflect Sequence Alignment Accuracy? Mol. Biol. Evol., August 1, 2008; 25(8): 1576 - 1580. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhao and R. J. Epstein Programmed Genetic Instability: A Tumor-Permissive Mechanism for Maintaining the Evolvability of Higher Species through Methylation-Dependent Mutation of DNA Repair Genes in the Male Germ Line Mol. Biol. Evol., August 1, 2008; 25(8): 1737 - 1749. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Dagan, Y. Artzy-Randrup, and W. Martin Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution PNAS, July 22, 2008; 105(29): 10039 - 10044. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Rival, E. Jaligot, T. Beule, and E. J. Finnegan Isolation and expression analysis of genes encoding MET, CMT, and DRM methyltransferases in oil palm (Elaeis guineensis Jacq.) in relation to the 'mantled' somaclonal variation J. Exp. Bot., July 17, 2008; (2008) ern178v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Zhu, Y.-B. Zhang, Q.-Y. Zhang, and J.-F. Gui Functional Domains and the Antiviral Effect of the Double-Stranded RNA-Dependent Protein Kinase PKR from Paralichthys olivaceus J. Virol., July 15, 2008; 82(14): 6889 - 6901. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. W. Singer, C. S. Chan, A. Zemla, N. C. VerBerkmoes, M. Hwang, R. L. Hettich, J. F. Banfield, and M. P. Thelen Characterization of Cytochrome 579, an Unusual Cytochrome Isolated from an Iron-Oxidizing Microbial Community Appl. Envir. Microbiol., July 15, 2008; 74(14): 4454 - 4462. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ueda, Y. Tagami, Y. Kamihara, H. Shiratori, H. Takano, and T. Beppu Isolation of Bacteria Whose Growth Is Dependent on High Levels of CO2 and Implications of Their Potential Diversity Appl. Envir. Microbiol., July 15, 2008; 74(14): 4535 - 4538. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Martinez-Aguilar, R. Diaz, J. J. Pena-Cabriales, P. Estrada-de los Santos, M. F. Dunn, and J. Caballero-Mellado Multichromosomal Genome Structure and Confirmation of Diazotrophy in Novel Plant-Associated Burkholderia Species Appl. Envir. Microbiol., July 15, 2008; 74(14): 4574 - 4579. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Quemeneur, A. Heinrich-Salmeron, D. Muller, D. Lievremont, M. Jauzein, P. N. Bertin, F. Garrido, and C. Joulian Diversity Surveys and Evolutionary Relationships of aoxB Genes in Aerobic Arsenite-Oxidizing Bacteria Appl. Envir. Microbiol., July 15, 2008; 74(14): 4567 - 4573. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Roca, E. Torrents, M. Sahlin, I. Gibert, and B.-M. Sjoberg NrdI Essentiality for Class Ib Ribonucleotide Reduction in Streptococcus pyogenes J. Bacteriol., July 15, 2008; 190(14): 4849 - 4858. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Gao and A. J. Francis Reduction of Uranium(VI) to Uranium(IV) by Clostridia Appl. Envir. Microbiol., July 15, 2008; 74(14): 4580 - 4584. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Ferrer-Admetlla, E. Bosch, M. Sikora, T. Marques-Bonet, A. Ramirez-Soriano, A. Muntasell, A. Navarro, R. Lazarus, F. Calafell, J. Bertranpetit, et al. Balancing Selection Is the Main Force Shaping the Evolution of Innate Immunity Genes J. Immunol., July 15, 2008; 181(2): 1315 - 1322. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. S. Campo, Z. Dimitrova, R. J. Mitchell, J. Lara, and Y. Khudyakov Coordinated evolution of the hepatitis C virus PNAS, July 15, 2008; 105(28): 9685 - 9690. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Das, M. T. Mazhab-Jafari, S. Chowdhury, S. SilDas, R. Selvaratnam, and G. Melacini Entropy-driven cAMP-dependent Allosteric Control of Inhibitory Interactions in Exchange Proteins Directly Activated by cAMP J. Biol. Chem., July 11, 2008; 283(28): 19691 - 19703. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J. Sanderson Phylogenetic Signal in the Eukaryotic Tree of Life Science, July 4, 2008; 321(5885): 121 - 123. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Verdone, R. Doliana, A. Corazza, S. A. Colebrooke, P. Spessotto, S. Bot, F. Bucciotti, A. Capuano, A. Silvestri, P. Viglino, et al. The Solution Structure of EMILIN1 Globular C1q Domain Reveals a Disordered Insertion Necessary for Interaction with the {alpha}4{beta}1 Integrin J. Biol. Chem., July 4, 2008; 283(27): 18947 - 18956. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Moroni, R. Vijayan, A. Carbone, R. Zwart, P. C. Biggin, and I. Bermudez Non-Agonist-Binding Subunit Interfaces Confer Distinct Functional Signatures to the Alternate Stoichiometries of the {alpha}4{beta}2 Nicotinic Receptor: An {alpha}4-{alpha}4 Interface Is Required for Zn2+ Potentiation J. Neurosci., July 2, 2008; 28(27): 6884 - 6894. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. E. Snook, B. J. Stafford, P. Li, G. Tan, L. Huang, R. Birbe, S. Schulz, M. J. Schnell, M. Thakur, J. L. Rothstein, et al. Guanylyl Cyclase C-Induced Immunotherapeutic Responses Opposing Tumor Metastases Without Autoimmunity J Natl Cancer Inst, July 2, 2008; 100(13): 950 - 961. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Thawai, S. Tanasupawat, and T. Kudo Micromonospora pattaloongensis sp. nov., isolated from a Thai mangrove forest Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1516 - 1521. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-Y. Weon, C.-M. Lee, S.-B. Hong, B.-Y. Kim, S.-H. Yoo, S.-W. Kwon, and S.-J. Go Kaistia soli sp. nov., isolated from a wetland in Korea Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1522 - 1524. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-Y. Weon, S.-H. Yoo, S.-B. Hong, S.-W. Kwon, E. Stackebrandt, S.-J. Go, and B.-S. Koo Polaromonas jejuensis sp. nov., isolated from soil in Korea Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1525 - 1528. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kageyama, A. Matsumoto, S. Omura, and Y. Takahashi Humibacillus xanthopallidus gen. nov., sp. nov. Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1547 - 1551. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Matsuyama, H. Katoh, T. Ohkushi, A. Satoh, K. Kawahara, and I. Yumoto Sphingobacterium kitahiroshimense sp. nov., isolated from soil Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1576 - 1579. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Yu. Sorokin, T. P. Tourova, G. Muyzer, and G. J. Kuenen Thiohalospira halophila gen. nov., sp. nov. and Thiohalospira alkaliphila sp. nov., novel obligately chemolithoautotrophic, halophilic, sulfur-oxidizing gammaproteobacteria from hypersaline habitats Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1685 - 1692. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. X. Han, E. T. Wang, L. J. Wu, W. F. Chen, J. G. Gu, C. T. Gu, C. F. Tian, and W. X. Chen Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1693 - 1699. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Mia Kim, D. L. Suarez, and C. L. Afonso Detection of a broad range of class I and II Newcastle disease viruses using a multiplex real-time reverse transcription polymerase chain reaction assay J Vet Diagn Invest, July 1, 2008; 20(4): 414 - 425. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Dang, X. Zhang, J. Sun, T. Li, Z. Zhang, and G. Yang Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea Microbiology, July 1, 2008; 154(7): 2084 - 2095. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Thirunavukkarasu, M. N. Mishra, S. Spaepen, J. Vanderleyden, C. A. Gross, and A. K. Tripathi An extra-cytoplasmic function sigma factor and anti-sigma factor control carotenoid biosynthesis in Azospirillum brasilense Microbiology, July 1, 2008; 154(7): 2096 - 2105. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Bleich, P. Kirsch, H. Sahly, J. Fahey, A. Smoczek, H.-J. Hedrich, and J. P Sundberg Klebsiella oxytoca: opportunistic infections in laboratory rodents Lab Anim, July 1, 2008; 42(3): 369 - 375. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Katoh and H. Toh Recent developments in the MAFFT multiple sequence alignment program Brief Bioinform, July 1, 2008; 9(4): 286 - 298. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. R. Duvall, J. W. Robinson, J. G. Mattson, and A. Moore Phylogenetic analyses of two mitochondrial metabolic genes sampled in parallel from angiosperms find fundamental interlocus incongruence Am. J. Botany, July 1, 2008; 95(7): 871 - 884. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Qin, D. W. Scott, and B. J. Mann Francisella tularensis subsp. tularensis Schu S4 Disulfide Bond Formation Protein B, but Not an RND-Type Efflux Pump, Is Required for Virulence Infect. Immun., July 1, 2008; 76(7): 3086 - 3092. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. C. M. Antunes, R. B. R. Ferreira, C. P. Lostroh, and E. P. Greenberg A Mutational Analysis Defines Vibrio fischeri LuxR Binding Sites J. Bacteriol., July 1, 2008; 190(13): 4392 - 4397. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. G. Remington, J. M. Crow, and J. D. Nelson Secretoglobins: Lacrimal Gland-Specific Rabbit Lipophilin mRNAs Invest. Ophthalmol. Vis. Sci., July 1, 2008; 49(7): 2856 - 2862. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Gayral, J.-C. Noa-Carrazana, M. Lescot, F. Lheureux, B. E. L. Lockhart, T. Matsumoto, P. Piffanelli, and M.-L. Iskra-Caruana A Single Banana Streak Virus Integration Event in the Banana Genome as the Origin of Infectious Endogenous Pararetrovirus J. Virol., July 1, 2008; 82(13): 6697 - 6710. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Feng, B. Liu, Y. Liu, Y. A. Ratiner, B. Hu, D. Li, X. Zong, W. Xiong, and L. Wang A Genomic Islet Mediates Flagellar Phase Variation in Escherichia coli Strains Carrying the Flagellin-Specifying Locus flk J. Bacteriol., July 1, 2008; 190(13): 4470 - 4477. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Munoz de Rueda, J. Casado, R. Paton, D. Quintero, A. Palacios, A. Gila, R. Quiles, J. Leon, A. Ruiz-Extremera, and J. Salmeron Mutations in E2-PePHD, NS5A-PKRBD, NS5A-ISDR, and NS5A-V3 of Hepatitis C Virus Genotype 1 and Their Relationships to Pegylated Interferon-Ribavirin Treatment Responses J. Virol., July 1, 2008; 82(13): 6644 - 6653. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. G. Preston, J. Murray, C. M. Preston, I. M. McDougall, and N. D. Stow The UL25 Gene Product of Herpes Simplex Virus Type 1 Is Involved in Uncoating of the Viral Genome J. Virol., July 1, 2008; 82(13): 6654 - 6666. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. T. C. Hodson, A. Lewin, L. Hederstedt, and N. E. Le Brun The Active-Site Cysteinyls and Hydrophobic Cavity Residues of ResA Are Important for Cytochrome c Maturation in Bacillus subtilis J. Bacteriol., July 1, 2008; 190(13): 4697 - 4705. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Shirai, Y. Tomaru, Y. Takao, H. Suzuki, T. Nagumo, and K. Nagasaki Isolation and Characterization of a Single-Stranded RNA Virus Infecting the Marine Planktonic Diatom Chaetoceros tenuissimus Meunier Appl. Envir. Microbiol., July 1, 2008; 74(13): 4022 - 4027. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Sisakova, L. K. Stanley, M. Weiserova, and M. D. Szczelkun A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I Nucleic Acids Res., July 1, 2008; 36(12): 3939 - 3949. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Yamasaki, S. G. Schroeder, H. Sanchez-Villeda, B. S. Gaut, and M. D. McMullen Empirical Analysis of Selection Screens for Domestication and Improvement Loci in Maize by Extended DNA Sequencing The Plant Genome, July 1, 2008; 1(1): 33 - 43. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. T. Ku, Y.-S. Huang, Y.-S. Wang, D. Ma, and K.-W. Yeh IbMADS1 (Ipomoea batatas MADS-box 1 gene) is Involved in Tuberous Root Initiation in Sweet Potato (Ipomoea batatas) Ann. Bot., July 1, 2008; 102(1): 57 - 67. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Ishida and W. S. Leal Chiral discrimination of the Japanese beetle sex pheromone and a behavioral antagonist by a pheromone-degrading enzyme PNAS, July 1, 2008; 105(26): 9076 - 9080. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Asai, H. Kiryu, M. Hamada, Y. Tabei, K. Sato, H. Matsui, Y. Sakakibara, G. Terai, and T. Mituyama Software.ncrna.org: web servers for analyses of RNA sequences Nucleic Acids Res., July 1, 2008; 36(suppl_2): W75 - W78. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Torarinsson and S. Lindgreen WAR: Webserver for aligning structural RNAs Nucleic Acids Res., July 1, 2008; 36(suppl_2): W79 - W84. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T.-H. Chang, J.-T. Horng, and H.-D. Huang RNALogo: a new approach to display structural RNA alignment Nucleic Acids Res., July 1, 2008; 36(suppl_2): W91 - W96. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-F. Chang, Y.-L. Huang, and C. L. Lu SARSA: a web tool for structural alignment of RNA using a structural alphabet Nucleic Acids Res., July 1, 2008; 36(suppl_2): W19 - W24. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|