Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach
| Autor: | Adi Doron-Faigenboim, Tal Pupko, Elana Erez, Eric Martz, Eran Bacharach, Adi Stern |
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| Jazyk: | angličtina |
| Rok vydání: | 2007 |
| Předmět: |
Models
Molecular Web server Molecular Sequence Data Inference Biology computer.software_genre Bayesian inference Bayes' theorem Negative selection Sequence Analysis Protein Genetics Animals Humans Computer Simulation Amino Acid Sequence Amino Acids Selection (genetic algorithm) Phylogeny Statistical hypothesis testing Internet Phylogenetic tree Computational Biology Proteins Bayes Theorem Articles Amino Acid Substitution Data mining computer Algorithms Software |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | Biologically significant sites in a protein may be identified by contrasting the rates of synonymous (K(s)) and non-synonymous (K(a)) 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 K(a) and K(s) (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. |
| Databáze: | OpenAIRE |
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