IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

被引：107

作者：

Paez-Espino, David ^{[1
]}

Roux, Simon ^{[1
]}

Chen, I-Min A. ^{[2
]}

Palaniappan, Krishna ^{[2
]}

Ratner, Anna ^{[2
]}

Chu, Ken ^{[2
]}

Huntemann, Marcel ^{[1
]}

Reddy, T. B. K. ^{[1
]}

Carles Pons, Joan ^{[3
]}

Llabres, Merce ^{[3
]}

Eloe-Fadrosh, Emiley A. ^{[1
]}

Ivanova, Natalia N. ^{[1
]}

Kyrpides, Nikos C. ^{[1
]}

机构：

[1] Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA

[2] Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, 1 Cyclotron Rd, Berkeley, CA USA

[3] Univ Balearic Isl, Dept Math & Comp Sci, Palma De Mallorca, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2019年 / 47卷 / D1期

关键词：

RESOURCE; VIRUSES; INSIGHTS; HOSTS; DNA;

D O I：

10.1093/nar/gky1127

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Integrated Microbial Genome/Virus (IMG/VR) system v.2.0 (https://img.jgi.doe.gov/vr/) is the largest publicly available data management and analysis platform dedicated to viral genomics. Since the last report published in the 2016, NAR Database Issue, the data has tripled in size and currently contains genomes of 8389 cultivated reference viruses, 12 498 previously published curated prophages derived from cultivated microbial isolates, and 735112 viral genomic fragments computationally predicted from assembled shotgun metagenomes. Nearly 60% of the viral genomes and genome fragments are clustered into 110384 viral Operational Taxonomic Units (vOTUs) with two or more members. To improve data quality and predictions of host specificity, IMG/VR v.2.0 now separates prokaryotic and eukaryotic viruses, utilizes known prophage sequences to improve taxonomic assignments, and provides viral genome quality scores based on the estimated genome completeness. New features also include enhanced BLAST search capabilities for external queries. Finally, geographic map visualization to locate user-selected viral genomes or genome fragments has been implemented and download options have been extended. All of these features make IMG/VR v.2.0 a key resource for the study of viruses.

引用

页码：D678 / D686

页数：9

共 33 条

[21] Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data [J].

Paez-Espino, David ;

Pavlopoulos, Georgios A. ;

Ivanova, Natalia N. ;

Kyrpides, Nikos C. .

NATURE PROTOCOLS, 2017, 12 (08) :1673-1682

[22] IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses [J].

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 ;

Reddy, T. B. K. ;

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. .

NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D457-D465

[23] Uncovering Earth's virome [J].

Paez-Espino, David ;

Eloe-Fadrosh, Emiley A. ;

Pavlopoulos, Georgios A. ;

Thomas, Alex D. ;

Huntemann, Marcel ;

Mikhailova, Natalia ;

Rubin, Edward ;

Ivanova, Natalia N. ;

Kyrpides, Nikos C. .

NATURE, 2016, 536 (7617) :425-+

[24] Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community [J].

Pickett, Brett E. ;

Greer, Douglas S. ;

Zhang, Yun ;

Stewart, Lucy ;

Zhou, Liwei ;

Sun, Guangyu ;

Gu, Zhiping ;

Kumar, Sanjeev ;

Zaremba, Sam ;

Larsen, Christopher N. ;

Jen, Wei ;

Klem, Edward B. ;

Scheuermann, Richard H. .

VIRUSES-BASEL, 2012, 4 (11) :3209-3226

[25] Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing [J].

Rosario, Karyna ;

Fierer, Noah ;

Miller, Shelly ;

Luongo, Julia ;

Breitbart, Mya .

ENVIRONMENTAL SCIENCE & TECHNOLOGY, 2018, 52 (03) :1014-1027

[26] Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses [J].

Roux, Simon ;

Brum, Jennifer R. ;

Dutilh, Bas E. ;

Sunagawa, Shinichi ;

Duhaime, Melissa B. ;

Loy, Alexander ;

Poulos, Bonnie T. ;

Solonenko, Natalie ;

Lara, Elena ;

Poulain, Julie ;

Pesant, Stephane ;

Kandels-Lewis, Stefanie ;

Dimier, Celine ;

Picheral, Marc ;

Searson, Sarah ;

Cruaud, Corinne ;

Alberti, Adriana ;

Duarte, Carlos M. ;

Gasol, Josep M. ;

Vaque, Dolors ;

Bork, Peer ;

Acinas, Silvia G. ;

Wincker, Patrick ;

Sullivan, Matthew B. .

NATURE, 2016, 537 (7622) :689-+

[27] Viral dark matter and virus-host interactions resolved from publicly available microbial genomes [J].

Roux, Simon ;

Hallam, Steven J. ;

Woyke, Tanja ;

Sullivan, Matthew B. .

ELIFE, 2015, 4

[28] Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection [J].

Seshadri, Rekha ;

Leahy, Sinead C. ;

Attwood, Graeme T. ;

Teh, Koon Hoong ;

Lambie, Suzanne C. ;

Cookson, Adrian L. ;

Eloe-Fadrosh, Emiley A. ;

Pavlopoulos, Georgios A. ;

Hadjithomas, Michalis ;

Varghese, Neha J. ;

Paez-Espino, David ;

Perry, Rechelle ;

Henderson, Gemma ;

Creevey, Christopher J. ;

Terrapon, Nicolas ;

Lapebie, Pascal ;

Drula, Elodie ;

Lombard, Vincent ;

Rubin, Edward ;

Kyrpides, Nikos C. ;

Henrissat, Bernard ;

Woyke, Tanja ;

Ivanova, Natalia N. ;

Kelly, William J. ;

Palevich, Nikola ;

Janssen, Peter H. ;

Ronimus, Ron S. ;

Noel, Samantha ;

Soni, Priya ;

Reilly, Kerri ;

Atherly, Todd ;

Ziemer, Cherie ;

Wright, Andre-Denis ;

Ishaq, Suzanne ;

Cotta, Michael ;

Thompson, Stephanie ;

Crosley, Katie ;

McKain, Nest ;

Wallace, R. John ;

Flint, Harry J. ;

Martin, Jennifer C. ;

Forster, Robert J. ;

Gruninger, Robert J. ;

McAllister, Tim ;

Gilbert, Rosalind ;

Ouwerkerk, Diane ;

Klieve, Athol ;

Al Jassim, Rafat ;

Denman, Stuart ;

McSweeney, Chris .

NATURE BIOTECHNOLOGY, 2018, 36 (04) :359-+

[29] The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes [J].

Shmakov, Sergey A. ;

Sitnik, Vassilii ;

Makarova, Kira S. ;

Wolf, Yuri I. ;

Severinov, Konstantin V. ;

Koonin, Eugene V. .

MBIO, 2017, 8 (05)

[30] Clustal Omega for making accurate alignments of many protein sequences [J].

Sievers, Fabian ;

Higgins, Desmond G. .

PROTEIN SCIENCE, 2018, 27 (01) :135-145

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