The MicrobesOnline web site for comparative genomics

被引：154

作者：

Alm, EJ

Huang, KH

Price, MN

Koche, RP

Keller, K

Dubchak, IL

Arkin, AP ^{[1
]}

机构：

[1] Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA

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

[3] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA

[4] Howard Hughes Med Inst, Berkeley, CA 94720 USA

来源：

GENOME RESEARCH | 2005年 / 15卷 / 07期

关键词：

D O I：

10.1101/gr.3844805

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：

At present, hundreds of microbial genomes have been sequenced, and hundreds more are currently in the pipeline. The Virtual Institute for Microbial Stress and Survival has developed a publicly available Suite of Web-based comparative genomic tools (http://www.microbesonline.org) designed to facilitate multispecies comparison among prokaryotes. Highlights of the MicrobesOnline Web site include operon and regulon predictions, a multispecies genome browser, a multispecies Gene Ontology browser, a comparative KEGG metabolic pathway viewer, a Bioinformatics Workbench for in-depth sequence analysis, and Gene Carts that allow users to save genes of interest for further study while they browse. In addition, we provide an interface for genome annotation, which like all of the tools reported here, is freely available to the scientific community.

引用

页码：1015 / 1022

页数：8

共 35 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2] PRINTS and its automatic supplement, prePRINTS [J].

Attwood, TK ;

Bradley, P ;

Flower, DR ;

Gaulton, A ;

Maudling, N ;

Mitchell, AL ;

Moulton, G ;

Nordle, A ;

Paine, K ;

Taylor, P ;

Uddin, A ;

Zygouri, C .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :400-402

[3] CRITICA: Coding region identification tool invoking comparative analysis [J].

Badger, JH ;

Olsen, GJ .

MOLECULAR BIOLOGY AND EVOLUTION, 1999, 16 (04) :512-524

[4] 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

[5]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkr1065, 10.1093/nar/gkh121]

[6] The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 [J].

Boeckmann, B ;

Bairoch, A ;

Apweiler, R ;

Blatter, MC ;

Estreicher, A ;

Gasteiger, E ;

Martin, MJ ;

Michoud, K ;

O'Donovan, C ;

Phan, I ;

Pilbout, S ;

Schneider, M .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :365-370

[7] Prolinks: a database of protein functional linkages derived from coevolution [J].

Bowers, PM ;

Pellegrini, M ;

Thompson, MJ ;

Fierro, J ;

Yeates, TO ;

Eisenberg, D .

GENOME BIOLOGY, 2004, 5 (05)

[8] The gene ontology annotation (GOA) project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro [J].

Camon, E ;

Magrane, M ;

Barrell, D ;

Binns, D ;

Fleischmann, W ;

Kersey, P ;

Mulder, N ;

Oinn, T ;

Maslen, J ;

Cox, A ;

Apweiler, R .

GENOME RESEARCH, 2003, 13 (04) :662-672

[9] The Jalview Java']Java alignment editor [J].

Clamp, M ;

Cuff, J ;

Searle, SM ;

Barton, GJ .

BIOINFORMATICS, 2004, 20 (03) :426-427

[10] Conservation of gene order: a fingerprint of proteins that physically interact [J].

Dandekar, T ;

Snel, B ;

Huynen, M ;

Bork, P .

TRENDS IN BIOCHEMICAL SCIENCES, 1998, 23 (09) :324-328

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