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

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/

BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain

“…We examined the domain architecture of brain-specific assemblies by assessing their corresponding Pfam A domain and family assignments (STAR Methods). By definition, domains are highly conserved sequence patterns that are presumed to represent independent folding units, whereas domain pairs in multi-domain proteins represent combinations of units operating in tandem (Cromar et al, 2016). In general, while rarely in majority, brainspecific protein domains and domain pairs were found to occur widely across the BraInMap (Figure 2J), suggesting they confer brain-specific functions.…”

“…Domain architectures for all mouse proteins were obtained from PhyloPro 2.0 (Cromar et al, 2016) for the longest peptide associated with each gene. Domain predictions are based on Hidden Markov Models of curated seed alignments comprising Pfam A Domains and Families.…”

“…Ortholog predictions for all proteins were obtained from PhyloPro 2.0 (Cromar et al, 2016) and clustered using Cluster 3.0 (City Block, Complete Linkage) to group proteins with similar phylogenetic conservation patterns across 164 taxa. Taxa were phylogenetically arranged and grouped into: Eukaryotes, Opisthokonts, Metazoans, Vertebrates, and Mammals.…”

Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR

“…2019 ) or SMART ( Letunic and Bork 2018 ), in order to infer domain interactions and help identify physical and functional relationships between proteins. The PhyloPro2.0 phylogenetic profile database allows the visualization of PFAM domain conservation through heatmaps generated for 164 eukaryotes and can display up to 1,000 genes at a time ( Cromar et al. 2016 ).…”

PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages

“…As increasing numbers of sequenced genomes have become available, a number of phylogenetic profile databases and tools for visualization of Eukarya phylogenetic profiles have been developed ( Cheng & Perocchi, 2015 ; Cromar et al, 2016 ; Ott et al, 2012 ; Sadreyev et al, 2015 ; Szklarczyk et al, 2015 ). After considering the computational efficiency and prediction power of the current methods and tools, here we propose a method and online tool, called PrePhyloPro (PPP), which combines multiple co-occurrency measures and utilizes top rank thresholds to determine potential linkages.…”