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Nucleic Acids Research 2005 33(Web Server Issue):W295-W298; doi:10.1093/nar/gki406
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Manipulating multiple sequence alignments via MaM and WebMaM

Can Alkan*, Eray Tüzün1, Jerome Buard2, Franck Lethiec3, Evan E. Eichler1, Jeffrey A. Bailey4 and S. Cenk Sahinalp5

Department of EECS, Case Western Reserve University Cleveland, OH, USA 1Department of Genome Sciences, University of Washington Seattle, WA, USA 2Institute of Human Genetics, CNRS UPR 1142 Montpellier, France 3Mèthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS UMR 2506 Montpellier, France 4Department of Genetics, Case Western Reserve University Cleveland, OH, USA 5Department of Computing Science, SFU Burnaby, BC, Canada

*To whom correspondence should be addressed. Tel: +1 604 2687040; Fax: +1 604 2913045; Email: calkan{at}cwru.edu

Received February 14, 2005. Revised March 21, 2005. Accepted March 21, 2005.

MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned genomics sequences using a variety of user identified programs, databases and/or tables. The program can extract subalignments, corresponding to these various regions of DNA to be analyzed independently or in conjunction with other elements of genomic DNA. Graphical displays further allow an assessment of sequence variation throughout these different regions of the aligned sequence, providing separate displays for their repeat, non-repeat and coding portions of genomic DNA. The program should facilitate the phylogenetic analysis and processing of different portions of genomic sequence as part of large-scale sequencing efforts. MaM source code is freely available for non-commercial use at http://compbio.cs.sfu.ca/MAM.htm; and the web interface WebMaM is hosted at http://atgc.lirmm.fr/mam.


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