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Nucleic Acids Research 2004 32(Web Server Issue):W41-W44; doi:10.1093/nar/gkh361
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences

Michael Brudno, Rasmus Steinkamp1 and Burkhard Morgenstern1,*

Department of Computer Science, Stanford University, Stanford, CA 94305, USA and 1 University of Göttingen, Institute of Microbiology and Genetics, Goldschmidtstrasse 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 9, 2004; Revised and Accepted March 1, 2004

Cross-species sequence comparison is a powerful approach to analyze functional sites in genomic sequences and many discoveries have been made based on genomic alignments. Herein, we present a WWW-based software system for multiple alignment of large genomic sequences. Our server utilizes the previously developed combination of CHAOS and DIALIGN to achieve both speed and alignment accuracy. CHAOS is a fast database search tool that creates a list of local sequence similarities. These are used by DIALIGN as anchor points to speed up the final alignment procedure. The resulting alignment is returned to the user in different formats together with a list of anchor points found by CHAOS. The CHAOS/DIALIGN software is freely available at http://dialign.gobics.de/chaos-dialign-submission.

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 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.


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