PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya.
Identifieur interne : 000246 ( Main/Exploration ); précédent : 000245; suivant : 000247PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya.
Auteurs : Graham L. Cromar [Oman] ; Anthony Zhao [Canada] ; Xuejian Xiong [Canada] ; Lakshmipuram S. Swapna [Canada] ; Noeleen Loughran [Canada] ; Hongyan Song [Canada] ; John Parkinson [Canada]Source :
- Database : the journal of biological databases and curation [ 1758-0463 ] ; 2016.
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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/.
DOI: 10.1093/database/baw013
PubMed: 26980519
Affiliations:
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Swapna</name><affiliation wicri:level="1"><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and.</nlm:affiliation><country>Canada</country><wicri:regionArea>Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4</wicri:regionArea><wicri:noRegion>ON M5G 0A4</wicri:noRegion></affiliation></author><author><name sortKey="Loughran, Noeleen" sort="Loughran, Noeleen" uniqKey="Loughran N" first="Noeleen" last="Loughran">Noeleen Loughran</name><affiliation wicri:level="1"><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and.</nlm:affiliation><country>Canada</country><wicri:regionArea>Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4</wicri:regionArea><wicri:noRegion>ON M5G 0A4</wicri:noRegion></affiliation></author><author><name sortKey="Song, Hongyan" sort="Song, Hongyan" uniqKey="Song H" first="Hongyan" last="Song">Hongyan Song</name><affiliation wicri:level="1"><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and.</nlm:affiliation><country>Canada</country><wicri:regionArea>Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4</wicri:regionArea><wicri:noRegion>ON M5G 0A4</wicri:noRegion></affiliation></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><affiliation wicri:level="4"><nlm: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.</nlm:affiliation><country wicri:rule="url">Canada</country><wicri:regionArea>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</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author></analytic><series><title level="j">Database : the journal of biological databases and curation</title><idno type="eISSN">1758-0463</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Conserved Sequence</term><term>Databases, Protein</term><term>Eukaryota (metabolism)</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term><term>Search Engine</term><term>Species Specificity</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Eukaryota</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Conserved Sequence</term><term>Databases, Protein</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term><term>Search Engine</term><term>Species Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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/.</div></front></TEI><affiliations><list><country><li>Canada</li><li>Oman</li></country><region><li>Ontario</li></region><settlement><li>Toronto</li></settlement><orgName><li>Université de Toronto</li></orgName></list><tree><country name="Oman"><noRegion><name sortKey="Cromar, Graham L" sort="Cromar, Graham L" uniqKey="Cromar G" first="Graham L" last="Cromar">Graham L. Cromar</name></noRegion></country><country name="Canada"><noRegion><name sortKey="Zhao, Anthony" sort="Zhao, Anthony" uniqKey="Zhao A" first="Anthony" last="Zhao">Anthony Zhao</name></noRegion><name sortKey="Loughran, Noeleen" sort="Loughran, Noeleen" uniqKey="Loughran N" first="Noeleen" last="Loughran">Noeleen Loughran</name><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><name sortKey="Song, Hongyan" sort="Song, Hongyan" uniqKey="Song H" first="Hongyan" last="Song">Hongyan Song</name><name sortKey="Swapna, Lakshmipuram S" sort="Swapna, Lakshmipuram S" uniqKey="Swapna L" first="Lakshmipuram S" last="Swapna">Lakshmipuram S. Swapna</name><name sortKey="Xiong, Xuejian" sort="Xiong, Xuejian" uniqKey="Xiong X" first="Xuejian" last="Xiong">Xuejian Xiong</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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