title: 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/.
authors.affiliation: Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and graham.cromar@gmail.com.
authors.forename: Graham L
authors.initials: GL
authors.lastname: Cromar
authors.affiliation: Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and.
authors.forename: Anthony
authors.initials: A
authors.lastname: Zhao
authors.affiliation: Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and.
authors.forename: Xuejian
authors.initials: X
authors.lastname: Xiong
authors.affiliation: Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and.
authors.forename: Lakshmipuram S
authors.initials: LS
authors.lastname: Swapna
authors.affiliation: Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and.
authors.forename: Noeleen
authors.initials: N
authors.lastname: Loughran
authors.affiliation: Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Song
authors.affiliation: Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and Departments of Biochemistry, Computer Science and Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada john.parkinson@utoronto.ca.
authors.forename: John
authors.initials: J
authors.lastname: Parkinson
mesh_terms: D017124:Conserved Sequence; D030562:Databases, Protein; D056890:Eukaryota / Q000378:metabolism*; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D057386:Search Engine; D013045:Species Specificity