PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya.

Graham L Cromar,Hongyan Song,John Parkinson,Xuejian Xiong,Noeleen Loughran,Anthony Zhao,Lakshmipuram S Swapna

doi:10.1093/database/baw013

Graham L Cromar, Hongyan Song + Show 5 more

Open Access

https://doi.org/10.1093/database/baw013

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Journal: Database	Publication Date: Jan 1, 2016
Citations: 12	License type: cc-by

Affiliation: Hospital for Sick Children, University of Toronto

Abstract

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/

Highlights

Phylogenetic profiling has been widely adopted as a method to visualize evolutionary conservation of genes/ proteins
EnsemblCompara GeneTrees, which is largely focused on vertebrates, allows the visualization of ortholog gains and losses in the context of a phylogenetic tree [4]
A number of caveats are associated with orthology detection [37, 38]

Summary

Introduction

Phylogenetic profiling has been widely adopted as a method to visualize evolutionary conservation of genes/ proteins. PhyloPro offers an advanced search option that allows users to specify a number of parameters for the analysis including: (i) choice of reference species, (ii) limit the range of target species, (iii) choose the similarity metric and clustering method used for clustering the resulting heatmap (if applicable), (iv) choose the type of view (as above) and (v) upload a text file corresponding to the proteins to be searched.

Results

Conclusion