The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions

被引：156

作者：

Markowitz, Victor M. ^{[1
]}

Szeto, Ernest ^{[1
]}

Palaniappan, Krishna ^{[1
]}

Grechkin, Yuri ^{[1
]}

Chu, Ken ^{[1
]}

Chen, I-Min A. ^{[1
]}

Dubchak, Inna ^{[2
]}

Anderson, Iain ^{[3
]}

Lykidis, Athanasios ^{[3
]}

Mavromatis, Konstantinos ^{[3
]}

Ivanova, Natalia N. ^{[3
]}

Kyrpides, Nikos C. ^{[3
]}

机构：

[1] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Lawrence Berkeley Lab, Genom Div, Berkeley, CA 94720 USA

[3] Joint Genome Inst, Dept Energy, Genome Biol Program, Walnut Creek, CA USA

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

关键词：

D O I：

10.1093/nar/gkm846

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 [生物化学与分子生物学]; 081704 [应用化学];

摘要：

The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMGs data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov.

引用

页码：D528 / D533

页数：6

共 22 条

[1]

The MicrobesOnline web site for comparative genomics [J].

Alm, EJ ;

Huang, KH ;

Price, MN ;

Koche, RP ;

Keller, K ;

Dubchak, IL ;

Arkin, AP .

GENOME RESEARCH, 2005, 15 (07) :1015-1022

[2]

The ENZYME database in 2000 [J].

Bairoch, A .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :304-305

[3]

The universal protein resource (UniProt) [J].

Bairoch, Amos ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Puy, Ghislaine Argoud ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

deCastro, Edouard ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

Dobrokhotov, Pavel ;

Dornevil, Dolnide ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Feuermann, Marc ;

Gehant, Sebastian ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

Ioannidis, Vassilios ;

Ivanyi, Ivan ;

James, Janet ;

Jain, Eric ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra ;

Lara, Vicente ;

Lemercier, Philippe ;

Le Saux, Virginie .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D193-D197

[4]

Bateman A, 2002, NUCLEIC ACIDS RES, V30, P276, DOI [10.1093/nar/gkr1065, 10.1093/nar/gkp985, 10.1093/nar/gkh121]

[5]

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats [J].

Bland, Charles ;

Ramsey, Teresa L. ;

Sabree, Fareedah ;

Lowe, Micheal ;

Brown, Kyndall ;

Kyrpides, Nikos C. ;

Hugenholtz, Philip .

BMC BIOINFORMATICS, 2007, 8 (1)

[6]

MetaCyc: a multiorganism database of metabolic pathways and enzymes [J].

Caspi, Ron ;

Foerster, Hartmut ;

Fulcher, Carol A. ;

Hopkinson, Rebecca ;

Ingraham, John ;

Kaipa, Pallavi ;

Krummenacker, Markus ;

Paley, Suzanne ;

Pick, John ;

Rhee, Seung Y. ;

Tissier, Christophe ;

Zhang, Peifen ;

Karp, Peter D. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D511-D516

[7]

Enzyme-specific profiles for genome annotation: PRIAM [J].

Claudel-Renard, C ;

Chevalet, C ;

Faraut, T ;

Kahn, D .

NUCLEIC ACIDS RESEARCH, 2003, 31 (22) :6633-6639

[8]

Locating proteins in the cell using TargetP, SignalP and related tools [J].

Emanuelsson, Olof ;

Brunak, Soren ;

von Heijne, Gunnar ;

Nielsen, Henrik .

NATURE PROTOCOLS, 2007, 2 (04) :953-971

[9]

VISTA: computational tools for comparative genomics [J].

Frazer, KA ;

Pachter, L ;

Poliakov, A ;

Rubin, EM ;

Dubchak, I .

NUCLEIC ACIDS RESEARCH, 2004, 32 :W273-W279

[10]

G. O. Consortium, 2004, Nucleic Acids Res, V32, pD258, DOI DOI 10.1093/NAR/GKH036

← 1 2 3 →