ArticleDatabase : the journal of biological databases and curation2016
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya.
Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- TreeProfiler: large-scale metadata profiling along gene and species trees.Molecular biology and evolution · 2026Article
- Vector semantics of multidomain protein architectures.Bioinformatics advances · 2026Article
- Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families.Genome biology and evolution · 2024Article
- ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii.PLoS computational biology · 2024Article
- Simulating domain architecture evolution.Bioinformatics (Oxford, England) · 2022Article
- Identifying protein function and functional links based on large-scale co-occurrence patterns.PloS one · 2022Article
- BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain.Cell systems · 2020Article
- Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters.Communications biology · 2019Article
- Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation.Genome biology · 2018Article
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7 authors.
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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/.
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