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Bioinformatics Advance Access published online on December 1, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm600
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence

Jacques Oberto *

Biologie Moléculaire du Gène chez les Extrêmophiles, Université Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR8621, 91405 Orsay Cedex, France

*To whom correspondence should be addressed. Dr. Jacques Oberto, E-mail: jacques.oberto{at}igmors.u-psud.fr


  Abstract

Summary: BAGET (Bacterial and Archaeal Gene Exploration Tool) is a web service designed to facilitate extraction, by molecular geneticists and phylogeneticists, of specific gene and protein sequences from completely determined prokaryotic genomes. Upon selection of a particular prokaryotic organism and gene, two levels of visual gene context information are provided on a single dynamic page: i) a graphical representation of a user defined portion of the chromosome centered on the gene of interest and ii) the DNA sequence of the query gene, of the immediate neighboring genes and the intergenic regions each identified by a consistent color code. The aminoacid sequence is provided for protein-coding query genes. Query results can be exported as a rich text format (RTF) word processor file for printing, archival or further analysis.

Availability: http://archaea.u-psud.fr/bin/baget.dll

Contact: jacques.oberto{at}igmors.u-psud.fr

Associate Editor: Prof. John Quackenbush

Received on September 13, 2007; revised on November 15, 2007; accepted on November 28, 2007

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