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

Abstract

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.

Comparative study of the P2X gene family in animals and plants

“…The K a /K s ratio of positive-selection sites is greater than 1, which indicates that these sites change rapidly during evolution. In order to analyze the changing rate of amino acid in each subtype, the CDS sequences in each subtype were submitted together to the SELECTON Server (http://selecton.tau.ac.il/) [43] using three different evolutionary models: M8 (beta + w>=1), M5, MEC with default value. Then, codon K a /K s scores of the reference sequence were downloaded and the table was summarized after calculating the average K a /K s scores and filtering positive-selection sites.…”

“…In order to explore how these P2X subtypes evolve after duplication events and the amino acid substitutions of these subtypes by selective pressures, we further investigated variable selective pressures among amino acid sites of the P2X. Putative CDS sequences of each group were submitted to the SELECTON Server (http://selecton.tau.ac.il/) [43]. We used three evolutionary models [M8 (beta + w>=1), M5 (gamma), MEC] to perform the tests.…”

Molecular Characterization of Two Endothelin Pathways in East African Cichlid Fishes

“…First, we ran the data on the Selecton Server (Doron-Faigenboim et al 2005;Stern et al 2007). LRTs were conducted between the M8 model (b and x s C 1), which enables positive selection, and the M8a (b and x s = 1; no positive selection) and M7 (only purifying selection) models.…”

Filogenia do Complexo Drosophila Buzzatii (Grupo Repleta): Inferências de Análises Multilocus Mitocondriais e Nucleares.

“…(Nei & Gobojori, 1986), aplicado para as sequências parciais do gene transformer, sugeriu que estas estão sob seleção purificadora (Tabela 4). Para confirmar esse resultado, a hipótese nula de evolução neutra foi testada também com uma metodologia de análise Bayesiana, que permite a identificação de seleção natural em aminoácidos específicos do gene (Stern et al 2007). Utilizando o modelo M8 (Yang et al 2000), foi detectada razão entre dn e ds (ω) maior do que um, indicativo de seleção direcional, para os seguintes aminoácidos : 7,40,50,71,76,79,85,86,89,106,107,129,130 e 131 (Tabela 5).…”

“…Utilizando o modelo M8 (Yang et al 2000), foi detectada razão entre dn e ds (ω) maior do que um, indicativo de seleção direcional, para os seguintes aminoácidos : 7,40,50,71,76,79,85,86,89,106,107,129,130 e 131 (Tabela 5). No entanto, o limite mínimo do intervalo de confiança de ω foi menor do que um para todos eles (Tabela 5), em não concordância com a hipótese de seleção direcional (Stern et al 2007). Além disso, quando os resultados do modelo M8 foram comparados com os resultados baseados nos modelos M8a (Swanson et al 2003) e M7 (Yang et al 2000), pelo teste da razão de máxima verossimilhança, o sinal de seleção positiva nos aminoácido citados anteriormente não foi estatisticamente significativo.…”