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