PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences

被引：10

作者：

D'Ascenzo, MD ^{[1
]}

Collmer, A

Martin, GB

机构：

[1] Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA

[2] Cornell Univ, Dept Plant Pathol, Ithaca, NY 14853 USA

来源：

NUCLEIC ACIDS RESEARCH | 2004年 / 32卷 / 10期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1093/nar/gkh615

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：

PeerGAD is a web-based database-driven application that allows community-wide peer-reviewed annotation of prokaryotic genome sequences. The application was developed to support the annotation of the Pseudomonas syringae pv. tomato strain DC3000 genome sequence and is easily portable to other genome sequence annotation projects. PeerGAD incorporates several innovative design and operation features and accepts annotations pertaining to gene naming, role classification, gene translation and annotation derivation. The annotator tool in PeerGAD is built around a genome browser that offers users the ability to search and navigate the genome sequence. Because the application encourages annotation of the genome sequence directly by researchers and relies on peer review, it circumvents the need for an annotation curator while providing added value to the annotation data. Support for the Gene Ontology(TM) vocabulary, a structured and controlled vocabulary used in classification of gene roles, is emphasized throughout the system. Here we present the underlying concepts integral to the functionality of PeerGAD.

引用

页码：3124 / 3135

页数：12

共 15 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] Automated genome sequence analysis and annotation [J].

Andrade, MA ;

Brown, NP ;

Leroy, C ;

Hoersch, S ;

de Daruvar, A ;

Reich, C ;

Franchini, A ;

Tamames, J ;

Valencia, A ;

Ouzounis, C ;

Sander, C .

BIOINFORMATICS, 1999, 15 (05) :391-412

[3]

Ashburner M, 2001, GENOME RES, V11, P1425

[4] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[5] The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000 [J].

Buell, CR ;

Joardar, V ;

Lindeberg, M ;

Selengut, J ;

Paulsen, IT ;

Gwinn, ML ;

Dodson, RJ ;

Deboy, RT ;

Durkin, AS ;

Kolonay, JF ;

Madupu, R ;

Daugherty, S ;

Brinkac, L ;

Beanan, MJ ;

Haft, DH ;

Nelson, WC ;

Davidsen, T ;

Zafar, N ;

Zhou, LW ;

Liu, J ;

Yuan, QP ;

Khouri, H ;

Fedorova, N ;

Tran, B ;

Russell, D ;

Berry, K ;

Utterback, T ;

Van Aken, SE ;

Feldblyum, TV ;

D'Ascenzo, M ;

Deng, WL ;

Ramos, AR ;

Alfano, JR ;

Cartinhour, S ;

Chatterjee, AK ;

Delaney, TP ;

Lazarowitz, SG ;

Martin, GB ;

Schneider, DJ ;

Tang, XY ;

Bender, CL ;

White, O ;

Fraser, CM ;

Collmer, A .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (18) :10181-10186

[6] Improved microbial gene identification with GLIMMER [J].

Delcher, AL ;

Harmon, D ;

Kasif, S ;

White, O ;

Salzberg, SL .

NUCLEIC ACIDS RESEARCH, 1999, 27 (23) :4636-4641

[7]

Furumichi M., 2002, Genome Inform, V13, P402, DOI DOI 10.11234/GI1990.13.402

[8] Automated annotation of microbial proteomes in SWISS-PROT [J].

Gattiker, A ;

Michoud, K ;

Rivoire, C ;

Auchincloss, AH ;

Coudert, E ;

Lima, T ;

Kersey, P ;

Pagni, M ;

Sigrist, CJA ;

Lachaize, C ;

Veuthey, AL ;

Gasteiger, E ;

Bairoch, A .

COMPUTATIONAL BIOLOGY AND CHEMISTRY, 2003, 27 (01) :49-58

[9]

Gerlt JA, 2000, GENOME BIOL, V1

[10]

Gerstein M, 2000, SCIENCE, V288, P1590

← 1 2 →