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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G. L. Winsor, T. Van Rossum, R. Lo, B. Khaira, M. D. Whiteside, R. E. W. Hancock, and F. S. L. Brinkman Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes Nucleic Acids Res., January 1, 2009; 37(suppl_1): D483 - D488. [Abstract] [Full Text] [PDF]
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E. Andres Leon, I. Ezkurdia, B. Garcia, A. Valencia, and D. Juan EcID. A database for the inference of functional interactions in E. coli Nucleic Acids Res., January 1, 2009; 37(suppl_1): D629 - D635. [Abstract] [Full Text] [PDF]
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M. A. Held, B. Penning, A. S. Brandt, S. A. Kessans, W. Yong, S. R. Scofield, and N. C. Carpita Small-interfering RNAs from natural antisense transcripts derived from a cellulose synthase gene modulate cell wall biosynthesis in barley PNAS, December 23, 2008; 105(51): 20534 - 20539. [Abstract] [Full Text] [PDF]
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J. Liu, P. B. Gurpur, and S. J. Kaufman Genetically Determined Proteolytic Cleavage Modulates {alpha}7{beta}1 Integrin Function J. Biol. Chem., December 19, 2008; 283(51): 35668 - 35678. [Abstract] [Full Text] [PDF]
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R. Shi, M. Pineda, E. Ajamian, Q. Cui, A. Matte, and M. Cygler Structure of L-Xylulose-5-Phosphate 3-Epimerase (UlaE) from the Anaerobic L-Ascorbate Utilization Pathway of Escherichia coli: Identification of a Novel Phosphate Binding Motif within a TIM Barrel Fold J. Bacteriol., December 15, 2008; 190(24): 8137 - 8144. [Abstract] [Full Text] [PDF]
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G. Phillips, B. El Yacoubi, B. Lyons, S. Alvarez, D. Iwata-Reuyl, and V. de Crecy-Lagard Biosynthesis of 7-Deazaguanosine-Modified tRNA Nucleosides: a New Role for GTP Cyclohydrolase I J. Bacteriol., December 15, 2008; 190(24): 7876 - 7884. [Abstract] [Full Text] [PDF]
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V. Parkash, V.-M. Leppanen, H. Virtanen, J. M. Jurvansuu, M. M. Bespalov, Y. A. Sidorova, P. Runeberg-Roos, M. Saarma, and A. Goldman The Structure of the Glial Cell Line-derived Neurotrophic Factor-Coreceptor Complex: INSIGHTS INTO RET SIGNALING AND HEPARIN BINDING J. Biol. Chem., December 12, 2008; 283(50): 35164 - 35172. [Abstract] [Full Text] [PDF]
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J. Teng, R. Goto, K. Iida, I. Kojima, and H. Iida Ion-channel blocker sensitivity of voltage-gated calcium-channel homologue Cch1 in Saccharomyces cerevisiae Microbiology, December 1, 2008; 154(12): 3775 - 3781. [Abstract] [Full Text] [PDF]
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O. Symmons, A. Varadi, and T. Aranyi How Segmental Duplications Shape Our Genome: Recent Evolution of ABCC6 and PKD1 Mendelian Disease Genes Mol. Biol. Evol., December 1, 2008; 25(12): 2601 - 2613. [Abstract] [Full Text] [PDF]
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R. Frommolt, S. Werner, H. Paulsen, R. Goss, C. Wilhelm, S. Zauner, U. G. Maier, A. R. Grossman, D. Bhattacharya, and M. Lohr Ancient Recruitment by Chromists of Green Algal Genes Encoding Enzymes for Carotenoid Biosynthesis Mol. Biol. Evol., December 1, 2008; 25(12): 2653 - 2667. [Abstract] [Full Text] [PDF]
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S. Isabel, E. Leblanc, M. Boissinot, D. K. Boudreau, M. Grondin, F. J. Picard, E. A. Martel, N. J. Parham, P. S. G. Chain, D. E. Bader, et al. Divergence among Genes Encoding the Elongation Factor Tu of Yersinia Species J. Bacteriol., November 15, 2008; 190(22): 7548 - 7558. [Abstract] [Full Text] [PDF]
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J. V. Kus, J. Kelly, L. Tessier, H. Harvey, D. G. Cvitkovitch, and L. L. Burrows Modification of Pseudomonas aeruginosa Pa5196 Type IV Pilins at Multiple Sites with D-Araf by a Novel GT-C Family Arabinosyltransferase, TfpW J. Bacteriol., November 15, 2008; 190(22): 7464 - 7478. [Abstract] [Full Text] [PDF]
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P. Guardado-Calvo, L. Vazquez-Iglesias, J. Martinez-Costas, A. L. Llamas-Saiz, G. Schoehn, G. C. Fox, X. L. Hermo-Parrado, J. Benavente, and M. J. van Raaij Crystal Structure of the Avian Reovirus Inner Capsid Protein {sigma}A J. Virol., November 15, 2008; 82(22): 11208 - 11216. [Abstract] [Full Text] [PDF]
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A. Mazurie, D. Bonchev, B. Schwikowski, and G. A. Buck Phylogenetic distances are encoded in networks of interacting pathways Bioinformatics, November 15, 2008; 24(22): 2579 - 2585. [Abstract] [Full Text] [PDF]
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M. J. Pearce, J. Mintseris, J. Ferreyra, S. P. Gygi, and K. H. Darwin Ubiquitin-Like Protein Involved in the Proteasome Pathway of Mycobacterium tuberculosis Science, November 14, 2008; 322(5904): 1104 - 1107. [Abstract] [Full Text] [PDF]
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M. Thein, I. Bunikis, K. Denker, C. Larsson, S. Cutler, M. Drancourt, T. G. Schwan, R. Mentele, F. Lottspeich, S. Bergstrom, et al. Oms38 Is the First Identified Pore-Forming Protein in the Outer Membrane of Relapsing Fever Spirochetes J. Bacteriol., November 1, 2008; 190(21): 7035 - 7042. [Abstract] [Full Text] [PDF]
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D. G. Scofield and M. Lynch Evolutionary Diversification of the Sm Family of RNA-Associated Proteins Mol. Biol. Evol., November 1, 2008; 25(11): 2255 - 2267. [Abstract] [Full Text] [PDF]
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