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Nucleic Acids Research 2006 34(Web Server issue):W382-W384; doi:10.1093/nar/gkl272
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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

SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis

Han Liang, Weihua Zhou1 and Laura F. Landweber2,*

Department of Chemistry, Princeton University Princeton, NJ 08544, USA 1 Princeton Plasma Physics Laboratory, Princeton University Princeton, NJ 08544, USA 2 Department of Ecology and Evolutionary Biology, Princeton University Princeton, NJ 08544, USA

*To whom correspondence should be addressed. Tel: +1 609 258 1947; Fax: +1 609 258 7892; Email: lfl{at}princeton.edu

Received February 14, 2006. Revised March 19, 2006. Accepted April 3, 2006.

We present a bioinformatic web server (SWAKK) for detecting amino acid sites or regions of a protein under positive selection. It estimates the ratio of non-synonymous to synonymous substitution rates (KA/KS) between a pair of protein-coding DNA sequences, by sliding a 3D window, or sphere, across one reference structure. The program displays the results on the 3D protein structure. In addition, for comparison or when a reference structure is unavailable, the server can also perform a sliding window analysis on the primary sequence. The SWAKK web server is available at http://oxytricha.princeton.edu/SWAKK/.


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