Nucleic Acids Research, 2003, Vol. 31, No. 13 3497-3500
© 2003 Oxford University Press
Multiple sequence alignment with the Clustal series of programs
European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany 1 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-Ken 411-8540, Japan 2 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK 3 Department of Biochemistry, University College Cork, Cork, Ireland 4 Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, (CNRS/INSERM/ULP), BP 10142, 67404 Illkirch Cedex, France
*To whom correspondence should be addressed. Tel: +33 388653200; Fax: +33 388653276; Email: julie{at}igbmc.u-strasbg.fr
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/).
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M. Letek, A. A. Ocampo-Sosa, M. Sanders, U. Fogarty, T. Buckley, D. P. Leadon, P. Gonzalez, M. Scortti, W. G. Meijer, J. Parkhill, et al. Evolution of the Rhodococcus equi vap Pathogenicity Island Seen through Comparison of Host-Associated vapA and vapB Virulence Plasmids J. Bacteriol., September 1, 2008; 190(17): 5797 - 5805. [Abstract] [Full Text] [PDF]
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A. Just, F. Butter, M. Trenkmann, T. Heitkam, M. Morl, and H. Betat A comparative analysis of two conserved motifs in bacterial poly(A) polymerase and CCA-adding enzyme Nucleic Acids Res., September 1, 2008; 36(16): 5212 - 5220. [Abstract] [Full Text] [PDF]
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V. Mustonen, J. Kinney, C. G. Callan Jr, and M. Lassig Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites PNAS, August 26, 2008; 105(34): 12376 - 12381. [Abstract] [Full Text] [PDF]
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C. G. Grummitt, F. M. Townsley, C. M. Johnson, A. J. Warren, and M. Bycroft Structural Consequences of Nucleophosmin Mutations in Acute Myeloid Leukemia J. Biol. Chem., August 22, 2008; 283(34): 23326 - 23332. [Abstract] [Full Text] [PDF]
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L. Pache, S. Venkataraman, V. S. Reddy, and G. R. Nemerow Structural Variations in Species B Adenovirus Fibers Impact CD46 Association J. Virol., August 15, 2008; 82(16): 7923 - 7931. [Abstract] [Full Text] [PDF]
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A. M. Land, T. B. Ball, M. Luo, R. Pilon, P. Sandstrom, J. E. Embree, C. Wachihi, J. Kimani, and F. A. Plummer Human Immunodeficiency Virus (HIV) Type 1 Proviral Hypermutation Correlates with CD4 Count in HIV-Infected Women from Kenya J. Virol., August 15, 2008; 82(16): 8172 - 8182. [Abstract] [Full Text] [PDF]
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C. J. Plante, K. M. Coe, and R. G. Plante Isolation of Surfactant-Resistant Bacteria from Natural, Surfactant-Rich Marine Habitats Appl. Envir. Microbiol., August 15, 2008; 74(16): 5093 - 5099. [Abstract] [Full Text] [PDF]
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R. M. Vanacore, A.-J. L. Ham, J.-P. Cartailler, M. Sundaramoorthy, P. Todd, V. Pedchenko, Y. Sado, D.-B. Borza, and B. G. Hudson A Role for Collagen IV Cross-links in Conferring Immune Privilege to the Goodpasture Autoantigen: STRUCTURAL BASIS FOR THE CRYPTICITY OF B CELL EPITOPES J. Biol. Chem., August 15, 2008; 283(33): 22737 - 22748. [Abstract] [Full Text] [PDF]
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R. Becker, B. Loll, and A. Meinhart Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II J. Biol. Chem., August 15, 2008; 283(33): 22659 - 22669. [Abstract] [Full Text] [PDF]
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P. D. Kiely, J. O'Callaghan, A. Abbas, and F. O'Gara Genetic analysis of genes involved in dipeptide metabolism and cytotoxicity in Pseudomonas aeruginosa PAO1 Microbiology, August 1, 2008; 154(8): 2209 - 2218. [Abstract] [Full Text] [PDF]
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M. Hadjifrangiskou and T. M. Koehler Intrinsic curvature associated with the coordinately regulated anthrax toxin gene promoters Microbiology, August 1, 2008; 154(8): 2501 - 2512. [Abstract] [Full Text] [PDF]
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J. F. Staropoli and J. A. Branda Cord Formation in a Clinical Isolate of Mycobacterium marinum J. Clin. Microbiol., August 1, 2008; 46(8): 2814 - 2816. [Abstract] [Full Text] [PDF]
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F. Bagnoli, M. Moschioni, C. Donati, V. Dimitrovska, I. Ferlenghi, C. Facciotti, A. Muzzi, F. Giusti, C. Emolo, A. Sinisi, et al. A Second Pilus Type in Streptococcus pneumoniae Is Prevalent in Emerging Serotypes and Mediates Adhesion to Host Cells J. Bacteriol., August 1, 2008; 190(15): 5480 - 5492. [Abstract] [Full Text] [PDF]
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J. R. Hall, K. R. Mitchell, O. Jackson-Weaver, A. S. Kooser, B. R. Cron, L. J. Crossey, and C. D. Takacs-Vesbach Molecular Characterization of the Diversity and Distribution of a Thermal Spring Microbial Community by Using rRNA and Metabolic Genes Appl. Envir. Microbiol., August 1, 2008; 74(15): 4910 - 4922. [Abstract] [Full Text] [PDF]
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H. S. Jung, S. Komatsu, M. Ikebe, and R. Craig Head-Head and Head-Tail Interaction: A General Mechanism for Switching Off Myosin II Activity in Cells Mol. Biol. Cell, August 1, 2008; 19(8): 3234 - 3242. [Abstract] [Full Text] [PDF]
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J. L. Knies, K. K. Dang, T. J. Vision, N. G. Hoffman, R. Swanstrom, and C. L. Burch Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites Mol. Biol. Evol., August 1, 2008; 25(8): 1778 - 1787. [Abstract] [Full Text] [PDF]
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L. Deluc, J. Bogs, A. R. Walker, T. Ferrier, A. Decendit, J.-M. Merillon, S. P. Robinson, and F. Barrieu The Transcription Factor VvMYB5b Contributes to the Regulation of Anthocyanin and Proanthocyanidin Biosynthesis in Developing Grape Berries Plant Physiology, August 1, 2008; 147(4): 2041 - 2053. [Abstract] [Full Text] [PDF]
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S. Puthiyaveetil, T. A. Kavanagh, P. Cain, J. A. Sullivan, C. A. Newell, J. C. Gray, C. Robinson, M. van der Giezen, M. B. Rogers, and J. F. Allen The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts PNAS, July 22, 2008; 105(29): 10061 - 10066. [Abstract] [Full Text] [PDF]
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M. Stoczko, J.-M. Frere, G. M. Rossolini, and J.-D. Docquier Functional Diversity among Metallo-{beta}-Lactamases: Characterization of the CAR-1 Enzyme of Erwinia carotovora Antimicrob. Agents Chemother., July 1, 2008; 52(7): 2473 - 2479. [Abstract] [Full Text] [PDF]
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