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 | [ description ] |
"ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms."
"ClustalX is a new windows interface for the widely-used progressive multiple sequence alignment
program ClustalW. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. ClustalX displays the sequence alignment in
a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment."
MultiClustal is a Perl script designed to automate the process of alignment parameter choice for ClustalW with the goal of generating high quality multiple sequence alignments. It requires ClustalW 1.74(or above) and Boxshade 3.31 (or above, download).
Parallel versions of ClustalW and ClustalX have been developed by SGI.
DbClustal (server) is a program for aligning sequences detected by database searches, which uses local alignment information to anchor the global multiple alignment. A website has been implemented proposing BlastP database searches with automatic alignment of the top hits by DbClustal. DbClustal forms part of the WU-Blast2 server at EBI. Another multiple sequence alignment program taking advantage of both local and global alignment is T-Coffee.
| [ about the method ] |
Thompson JD, Higgins DG, and Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673-80.[Pubmed]
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, and Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997 Dec 15;25(24):4876-82.[Pubmed]
Yuan J, Amend A, Borkowski J, DeMarco R, Bailey W, Liu Y, Xie G, Blevins R. MULTICLUSTAL: a systematic method for surveying Clustal W alignment parameters.Bioinformatics 1999 Oct;15(10):862-3.[Pubmed]
Mikhailov D, Cofer H, and Gomperts R. Performance optimization of Clustal W: parallel Clustal W, HT Clustal, and MULTICLUSTAL.[SGI]
| [ documentation ] |
Version 1.83 and parallel version 1.81 of ClustalW/ClustalX and version 1.1 of MultiClustal are currently installed in our system. The Manual provided by the Author and example usage in our local system are listed below.
| [ availability ] |
Clustal Serieslocal installation
[ access Clustal Series]
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Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]
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| | Dec 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Fabien Campagne; ICB Conference Room - Y.1301
Jan 15th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Lei Shi; ICB Conference Room - Y.1301
Feb 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Christopher E. Mason; ICB Conference Room - Y.1301
Mar 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Olivier Elemento; ICB Conference Room - Y.1301
Apr 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Emre Aksay; ICB Conference Room - Y.1301
May 14th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Jonathan D. Victor; ICB Conference Room - Y.1301
Jun 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Harel Weinstein; ICB Conference Room - Y.1301
Jul 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Duane Hassane; ICB Conference Room - Y.1301
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