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Nucleic Acids Research 2005 33(Web Server Issue):W532-W534; doi:10.1093/nar/gki386
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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

Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC

Dirk Pöhler, Nadine Werner, Rasmus Steinkamp and Burkhard Morgenstern*

Institute of Microbiology and Genetics, University of Göttingen Goldschmidtstr. 1, 37077 Göttingen, Germany

*To whom correspondence should be addressed. Tel: +49 551 39 14628; Fax: +49 551 39 14929; Email: bmorgen{at}gwdg.de

Received February 14, 2005. Revised March 9, 2005. Accepted March 9, 2005.

Comparative analysis of genomic sequences is a powerful approach to discover functional sites in these sequences. Herein, we present a WWW-based software system for multiple alignment of genomic sequences. We use the local alignment tool CHAOS to rapidly identify chains of pairwise similarities. These similarities are used as anchor points to speed up the DIALIGN multiple-alignment program. Finally, the visualization tool ABC is used for interactive graphical representation of the resulting multiple alignments. Our software is available at Göttingen Bioinformatics Compute Server (GOBICS) at http://dialign.gobics.de/chaos-dialign-submission

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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