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Bioinformatics Advance Access published online on August 26, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn441
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GOfetcher: A Database with Complex Searching Facility for Gene Ontology

Mehdi Pirooznia 1, Tanwir Habib 1, Edward J Perkins 2 and Youping Deng 1,*

1Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, 39406, USA
2Environmental Laboratory, U.S., Army Engineer Research and Development Center, Vicksburg, Mississippi 39180, USA

*To whom correspondence should be addressed. Dr. Mehdi Pirooznia, E-mail: pirooznia{at}gmail.com


  Abstract

Motivation:An important contribution to the Gene Ontology (GO) project is to develop tools that facilitate the creation, maintenance and use of ontologies. Several tools have been created for communicating and using the GO project. However, a limitation with most of these tools is that they suffer from lack of a comprehensive search facility. We developed a web application, GOfetcher, with a very comprehensive search facility for the GO project and a variety of output formats for the results. GOfetcher has three different levels for searching the GO: ‘Quick Search’, ‘Advanced Search’, and ‘Upload Files’ for searching. The application includes a unique search option which generates gene information given a nucleotide or protein accession number which can then be used in generating gene ontology information. The output data in GOfetcher can be saved into several different formats; including spreadsheet, comma-separated values, and the Extensible Markup Language (XML) format. The database is available at http://mcbc.usm.edu/gofetcher/

Associate Editor: Prof. Dmitrij Frishman

Received on March 4, 2008; revised on May 29, 2008; accepted on August 18, 2008

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