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Published online 7 June 2004

Nucleic Acids Research, 2004, Vol. 32, No. 10 3124-3135
© 2004 Oxford University Press

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

Mark D. D’Ascenzo*,1, Alan Collmer2 and Gregory B. Martin1,2

1 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA and 2 Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA

*To whom correspondence should be addressed. Tel: +1 607 254 8795; Fax: +1 607 255 6695; Email: mdd9{at}cornell.edu

Received January 9, 2004; Revised April 1, 2004; Accepted April 27, 2004

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 OntologyTM 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.


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