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IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.
Paez-Espino, David; Chen, I-Min A; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Huang, Jinghua; Markowitz, Victor M; Nielsen, Torben; Huntemann, Marcel; K Reddy, T B; Pavlopoulos, Georgios A; Sullivan, Matthew B; Campbell, Barbara J; Chen, Feng; McMahon, Katherine; Hallam, Steve J; Denef, Vincent; Cavicchioli, Ricardo; Caffrey, Sean M; Streit, Wolfgang R; Webster, John; Handley, Kim M; Salekdeh, Ghasem H; Tsesmetzis, Nicolas; Setubal, Joao C; Pope, Phillip B; Liu, Wen-Tso; Rivers, Adam R; Ivanova, Natalia N; Kyrpides, Nikos C.
Afiliación
  • Paez-Espino D; Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
  • Chen IA; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
  • Palaniappan K; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
  • Ratner A; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
  • Chu K; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
  • Szeto E; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
  • Pillay M; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
  • Huang J; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
  • Markowitz VM; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
  • Nielsen T; Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
  • Huntemann M; Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
  • K Reddy TB; Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
  • Pavlopoulos GA; Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
  • Sullivan MB; Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA.
  • Campbell BJ; Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA.
  • Chen F; Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA.
  • McMahon K; Department of Civil and Environmental Engineering, Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.
  • Hallam SJ; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
  • Denef V; Genome Science, Technology, and Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
  • Cavicchioli R; Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, BC V6T 1Z2, Canada.
  • Caffrey SM; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 0A1, Canada.
  • Streit WR; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA.
  • Webster J; School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
  • Handley KM; Department of Biological Sciences, University of Calgary, Calgary, AB T2N 4V8, Canada.
  • Salekdeh GH; Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg 22609, Germany.
  • Tsesmetzis N; School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
  • Setubal JC; School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
  • Pope PB; Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj 31535-1897, Iran.
  • Liu WT; Shell International Exploration and Production Inc., Houston, TX 77082, USA.
  • Rivers AR; Department of Biochemistry, Institute of Chemistry, Universidade de Sao Paulo, SP 05508-000, Brazil.
  • Ivanova NN; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1432, Norway.
  • Kyrpides NC; Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Nucleic Acids Res ; 45(D1): D457-D465, 2017 01 04.
Article en En | MEDLINE | ID: mdl-27799466
ABSTRACT
Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https//img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Retroviridae / Programas Informáticos / Genoma Viral / Genómica / Bases de Datos Genéticas / Virus ADN / Metagenómica Idioma: En Revista: Nucleic Acids Res Año: 2017 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Retroviridae / Programas Informáticos / Genoma Viral / Genómica / Bases de Datos Genéticas / Virus ADN / Metagenómica Idioma: En Revista: Nucleic Acids Res Año: 2017 Tipo del documento: Article País de afiliación: Estados Unidos