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PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles
Proteins that function in the same pathways, protein complexes or the same environmental conditions can show similar patterns of sequence conservation across phylogenetic clades. In species that no longer require a specific protein complex or pathway, these proteins, as a group, tend to be lost or d...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489270/ https://www.ncbi.nlm.nih.gov/pubmed/25958392 http://dx.doi.org/10.1093/nar/gkv452 |
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author | Sadreyev, Ilyas R. Ji, Fei Cohen, Emiliano Ruvkun, Gary Tabach, Yuval |
author_facet | Sadreyev, Ilyas R. Ji, Fei Cohen, Emiliano Ruvkun, Gary Tabach, Yuval |
author_sort | Sadreyev, Ilyas R. |
collection | PubMed |
description | Proteins that function in the same pathways, protein complexes or the same environmental conditions can show similar patterns of sequence conservation across phylogenetic clades. In species that no longer require a specific protein complex or pathway, these proteins, as a group, tend to be lost or diverge. Analysis of the similarity in patterns of sequence conservation across a large set of eukaryotes can predict functional associations between different proteins, identify new pathway members and reveal the function of previously uncharacterized proteins. We used normalized phylogenetic profiling to predict protein function and identify new pathway members and disease genes. The phylogenetic profiles of tens of thousands conserved proteins in the human, mouse, Caenorhabditis elegans and Drosophila genomes can be queried on our new web server, PhyloGene. PhyloGene provides intuitive and user-friendly platform to query the patterns of conservation across 86 animal, fungal, plant and protist genomes. A protein query can be submitted either by selecting the name from whole-genome protein sets of the intensively studied species or by entering a protein sequence. The graphic output shows the profile of sequence conservation for the query and the most similar phylogenetic profiles for the proteins in the genome of choice. The user can also download this output in numerical form. |
format | Online Article Text |
id | pubmed-4489270 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-44892702015-07-07 PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles Sadreyev, Ilyas R. Ji, Fei Cohen, Emiliano Ruvkun, Gary Tabach, Yuval Nucleic Acids Res Web Server issue Proteins that function in the same pathways, protein complexes or the same environmental conditions can show similar patterns of sequence conservation across phylogenetic clades. In species that no longer require a specific protein complex or pathway, these proteins, as a group, tend to be lost or diverge. Analysis of the similarity in patterns of sequence conservation across a large set of eukaryotes can predict functional associations between different proteins, identify new pathway members and reveal the function of previously uncharacterized proteins. We used normalized phylogenetic profiling to predict protein function and identify new pathway members and disease genes. The phylogenetic profiles of tens of thousands conserved proteins in the human, mouse, Caenorhabditis elegans and Drosophila genomes can be queried on our new web server, PhyloGene. PhyloGene provides intuitive and user-friendly platform to query the patterns of conservation across 86 animal, fungal, plant and protist genomes. A protein query can be submitted either by selecting the name from whole-genome protein sets of the intensively studied species or by entering a protein sequence. The graphic output shows the profile of sequence conservation for the query and the most similar phylogenetic profiles for the proteins in the genome of choice. The user can also download this output in numerical form. Oxford University Press 2015-07-01 2015-05-09 /pmc/articles/PMC4489270/ /pubmed/25958392 http://dx.doi.org/10.1093/nar/gkv452 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Web Server issue Sadreyev, Ilyas R. Ji, Fei Cohen, Emiliano Ruvkun, Gary Tabach, Yuval PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles |
title | PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles |
title_full | PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles |
title_fullStr | PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles |
title_full_unstemmed | PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles |
title_short | PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles |
title_sort | phylogene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles |
topic | Web Server issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489270/ https://www.ncbi.nlm.nih.gov/pubmed/25958392 http://dx.doi.org/10.1093/nar/gkv452 |
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