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TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites
Understanding species adaptation at the molecular level has been a central goal of evolutionary biology and genomics research. This important task becomes increasingly relevant with the constant rise in both genotypic and phenotypic data availabilities. The TraitRateProp web server offers a unique p...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570260/ https://www.ncbi.nlm.nih.gov/pubmed/28453644 http://dx.doi.org/10.1093/nar/gkx288 |
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author | Levy Karin, Eli Ashkenazy, Haim Wicke, Susann Pupko, Tal Mayrose, Itay |
author_facet | Levy Karin, Eli Ashkenazy, Haim Wicke, Susann Pupko, Tal Mayrose, Itay |
author_sort | Levy Karin, Eli |
collection | PubMed |
description | Understanding species adaptation at the molecular level has been a central goal of evolutionary biology and genomics research. This important task becomes increasingly relevant with the constant rise in both genotypic and phenotypic data availabilities. The TraitRateProp web server offers a unique perspective into this task by allowing the detection of associations between sequence evolution rate and whole-organism phenotypes. By analyzing sequences and phenotypes of extant species in the context of their phylogeny, it identifies sequence sites in a gene/protein whose evolutionary rate is associated with shifts in the phenotype. To this end, it considers alternative histories of whole-organism phenotypic changes, which result in the extant phenotypic states. Its joint likelihood framework that combines models of sequence and phenotype evolution allows testing whether an association between these processes exists. In addition to predicting sequence sites most likely to be associated with the phenotypic trait, the server can optionally integrate structural 3D information. This integration allows a visual detection of trait-associated sequence sites that are juxtapose in 3D space, thereby suggesting a common functional role. We used TraitRateProp to study the shifts in sequence evolution rate of the RPS8 protein upon transitions into heterotrophy in Orchidaceae. TraitRateProp is available at http://traitrate.tau.ac.il/prop. |
format | Online Article Text |
id | pubmed-5570260 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-55702602017-08-29 TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites Levy Karin, Eli Ashkenazy, Haim Wicke, Susann Pupko, Tal Mayrose, Itay Nucleic Acids Res Web Server Issue Understanding species adaptation at the molecular level has been a central goal of evolutionary biology and genomics research. This important task becomes increasingly relevant with the constant rise in both genotypic and phenotypic data availabilities. The TraitRateProp web server offers a unique perspective into this task by allowing the detection of associations between sequence evolution rate and whole-organism phenotypes. By analyzing sequences and phenotypes of extant species in the context of their phylogeny, it identifies sequence sites in a gene/protein whose evolutionary rate is associated with shifts in the phenotype. To this end, it considers alternative histories of whole-organism phenotypic changes, which result in the extant phenotypic states. Its joint likelihood framework that combines models of sequence and phenotype evolution allows testing whether an association between these processes exists. In addition to predicting sequence sites most likely to be associated with the phenotypic trait, the server can optionally integrate structural 3D information. This integration allows a visual detection of trait-associated sequence sites that are juxtapose in 3D space, thereby suggesting a common functional role. We used TraitRateProp to study the shifts in sequence evolution rate of the RPS8 protein upon transitions into heterotrophy in Orchidaceae. TraitRateProp is available at http://traitrate.tau.ac.il/prop. Oxford University Press 2017-07-03 2017-04-27 /pmc/articles/PMC5570260/ /pubmed/28453644 http://dx.doi.org/10.1093/nar/gkx288 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Web Server Issue Levy Karin, Eli Ashkenazy, Haim Wicke, Susann Pupko, Tal Mayrose, Itay TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites |
title | TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites |
title_full | TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites |
title_fullStr | TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites |
title_full_unstemmed | TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites |
title_short | TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites |
title_sort | traitrateprop: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570260/ https://www.ncbi.nlm.nih.gov/pubmed/28453644 http://dx.doi.org/10.1093/nar/gkx288 |
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