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Nucleic Acids Research 2006 34(Web Server issue):W613-W616; doi:10.1093/nar/gkl288
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© The Author 2006. 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@oxfordjournals.org

Article

AliWABA: alignment on the web through an A-Bruijn approach

Neil C. Jones, Degui Zhi and Benjamin J. Raphael*

Department of Computer Science and Engineering, University of California San Diego La Jolla, CA, USA

*To whom correspondence should be addressed. Tel: +1 858 534 9989; Fax: +1 858 534 7029; Email: braphael{at}cs.uscd.edu

Received February 14, 2006. Revised March 1, 2006. Accepted April 5, 2006.

Multiple sequence alignment programs are an invaluable tool in computational biology. A-Bruijn Alignment (ABA) is a method for multiple sequence alignment that represents an alignment as a directed graph and has proved useful in aligning nucleotide and amino acid sequences that are composed of repeated and shuffled subsequences. AliWABA is a web server that provides tools to generate alignments with ABA, visualize the resulting ABA graphs and extract subsequences from ABA graphs. AliWABA greatly simplifies the problem of analyzing multiple sequences for local similarities that may be reordered, as is common with the domain architectures of proteins. To facilitate the analysis of protein domains, AliWABA provides direct querying of the Conserved Domain Database. Availability: http://aba.nbcr.net/

*Correspondence may also be addressed to Neil C. Jones. Email: ncjones{at}cs.uscd.edu


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