Cargando…
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya
PhyloPro is a database and accompanying web-based application for the construction and exploration of phylogenetic profiles across the Eukarya. In this update article, we present six major new developments in PhyloPro: (i) integration of Pfam-A domain predictions for all proteins; (ii) new summary h...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792532/ https://www.ncbi.nlm.nih.gov/pubmed/26980519 http://dx.doi.org/10.1093/database/baw013 |
_version_ | 1782421257783869440 |
---|---|
author | Cromar, Graham L. Zhao, Anthony Xiong, Xuejian Swapna, Lakshmipuram S. Loughran, Noeleen Song, Hongyan Parkinson, John |
author_facet | Cromar, Graham L. Zhao, Anthony Xiong, Xuejian Swapna, Lakshmipuram S. Loughran, Noeleen Song, Hongyan Parkinson, John |
author_sort | Cromar, Graham L. |
collection | PubMed |
description | PhyloPro is a database and accompanying web-based application for the construction and exploration of phylogenetic profiles across the Eukarya. In this update article, we present six major new developments in PhyloPro: (i) integration of Pfam-A domain predictions for all proteins; (ii) new summary heatmaps and detailed level views of domain conservation; (iii) an interactive, network-based visualization tool for exploration of domain architectures and their conservation; (iv) ability to browse based on protein functional categories (GOSlim); (v) improvements to the web interface to enhance drill down capability from the heatmap view; and (vi) improved coverage including 164 eukaryotes and 12 reference species. In addition, we provide improved support for downloading data and images in a variety of formats. Among the existing tools available for phylogenetic profiles, PhyloPro provides several innovative domain-based features including a novel domain adjacency visualization tool. These are designed to allow the user to identify and compare proteins with similar domain architectures across species and thus develop hypotheses about the evolution of lineage-specific trajectories. Database URL: http://www.compsysbio.org/phylopro/ |
format | Online Article Text |
id | pubmed-4792532 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-47925322016-03-16 PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya Cromar, Graham L. Zhao, Anthony Xiong, Xuejian Swapna, Lakshmipuram S. Loughran, Noeleen Song, Hongyan Parkinson, John Database (Oxford) Original Article PhyloPro is a database and accompanying web-based application for the construction and exploration of phylogenetic profiles across the Eukarya. In this update article, we present six major new developments in PhyloPro: (i) integration of Pfam-A domain predictions for all proteins; (ii) new summary heatmaps and detailed level views of domain conservation; (iii) an interactive, network-based visualization tool for exploration of domain architectures and their conservation; (iv) ability to browse based on protein functional categories (GOSlim); (v) improvements to the web interface to enhance drill down capability from the heatmap view; and (vi) improved coverage including 164 eukaryotes and 12 reference species. In addition, we provide improved support for downloading data and images in a variety of formats. Among the existing tools available for phylogenetic profiles, PhyloPro provides several innovative domain-based features including a novel domain adjacency visualization tool. These are designed to allow the user to identify and compare proteins with similar domain architectures across species and thus develop hypotheses about the evolution of lineage-specific trajectories. Database URL: http://www.compsysbio.org/phylopro/ Oxford University Press 2016-03-15 /pmc/articles/PMC4792532/ /pubmed/26980519 http://dx.doi.org/10.1093/database/baw013 Text en © The Author(s) 2016. Published by Oxford University Press. 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 | Original Article Cromar, Graham L. Zhao, Anthony Xiong, Xuejian Swapna, Lakshmipuram S. Loughran, Noeleen Song, Hongyan Parkinson, John PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya |
title | PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya |
title_full | PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya |
title_fullStr | PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya |
title_full_unstemmed | PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya |
title_short | PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya |
title_sort | phylopro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the eukarya |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792532/ https://www.ncbi.nlm.nih.gov/pubmed/26980519 http://dx.doi.org/10.1093/database/baw013 |
work_keys_str_mv | AT cromargrahaml phylopro20adatabaseforthedynamicexplorationofphylogeneticallyconservedproteinsandtheirdomainarchitecturesacrosstheeukarya AT zhaoanthony phylopro20adatabaseforthedynamicexplorationofphylogeneticallyconservedproteinsandtheirdomainarchitecturesacrosstheeukarya AT xiongxuejian phylopro20adatabaseforthedynamicexplorationofphylogeneticallyconservedproteinsandtheirdomainarchitecturesacrosstheeukarya AT swapnalakshmipurams phylopro20adatabaseforthedynamicexplorationofphylogeneticallyconservedproteinsandtheirdomainarchitecturesacrosstheeukarya AT loughrannoeleen phylopro20adatabaseforthedynamicexplorationofphylogeneticallyconservedproteinsandtheirdomainarchitecturesacrosstheeukarya AT songhongyan phylopro20adatabaseforthedynamicexplorationofphylogeneticallyconservedproteinsandtheirdomainarchitecturesacrosstheeukarya AT parkinsonjohn phylopro20adatabaseforthedynamicexplorationofphylogeneticallyconservedproteinsandtheirdomainarchitecturesacrosstheeukarya |