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Nucleic Acids Research Advance Access published online on June 22, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm382
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach

Adi Stern1, Adi Doron-Faigenboim1, Elana Erez1, Eric Martz2, Eran Bacharach1 and Tal Pupko1,*

1Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel and 2Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA

*To whom correspondence should be addressed. Tel: 972-3-640-7693; Fax: 972-3-642-2046; Email: talp{at}post.tau.ac.il

Received January 31, 2007. Revised April 15, 2007. Accepted April 30, 2007.

Biologically significant sites in a protein may be identified by contrasting the rates of synonymous (Ks) and non-synonymous (Ka) substitutions. This enables the inference of site-specific positive Darwinian selection and purifying selection. We present here Selecton version 2.2 (http://selecton.bioinfo.tau.ac.il), a web server which automatically calculates the ratio between Ka and Ks ({omega}) at each site of the protein. This ratio is graphically displayed on each site using a color-coding scheme, indicating either positive selection, purifying selection or lack of selection. Selecton implements an assembly of different evolutionary models, which allow for statistical testing of the hypothesis that a protein has undergone positive selection. Specifically, the recently developed mechanistic-empirical model is introduced, which takes into account the physicochemical properties of amino acids. Advanced options were introduced to allow maximal fine tuning of the server to the user's specific needs, including calculation of statistical support of the {omega} values, an advanced graphic display of the protein's 3-dimensional structure, use of different genetic codes and inputting of a pre-built phylogenetic tree. Selecton version 2.2 is an effective, user-friendly and freely available web server which implements up-to-date methods for computing site-specific selection forces, and the visualization of these forces on the protein's sequence and structure.

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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