Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.
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DOI：
10.1093/nar/gkm382
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发表时间：
2007-07
影响因子：
14.9
通讯作者：
Pupko, Tal
中科院分区：
文献类型：
--
作者：
Stern, Adi;Doron-Faigenboim, Adi;Erez, Elana;Martz, Eric;Bacharach, Eran;Pupko, Tal
可以通过对比同义(Ks)和非同义(Ka)替换的比率来确定蛋白质中具有生物学意义的位置。这使得对特定位点的正达尔文选择和纯化选择的推断成为可能。我们在这里提出了选择版本2.2(http://selecton.bioinfo.tau.ac.il)，)，这是一种网络服务器，它自动计算蛋白质每个位置上的Ka和Ks之间的比率(ω)。该比率使用颜色编码方案以图形方式显示在每个站点上，表示选择是肯定的、是纯净的选择，还是缺少选择。选择素实现了不同进化模型的组合，这允许对蛋白质经历了正向选择的假设进行统计测试。具体地说，介绍了最近发展起来的考虑氨基酸的物理化学性质的机理-经验模型。采用了先进的选项，以便最大限度地微调服务器以满足用户的具体需要，包括计算ω值的统计支持度、先进的蛋白质三维结构的图形显示、使用不同的遗传密码和输入预先建立的系统发育树。Selecton版本2.2是一个有效的、用户友好的、可免费获得的Web服务器，它实现了计算特定位点的选择力的最新方法，并将这些力可视化地显示在蛋白质的序列和结构上。
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 (ω) 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 ω 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.