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Bioinformatics Advance Access published online on January 19, 2007
Bioinformatics, doi:10.1093/bioinformatics/btl682
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

AphidBase: a database for aphid genomic resources

Jean-Pierre Gauthier 1, Fabrice Legeai 2, Alain Zasadzinski 3, Claude Rispe 1 and Denis Tagu 1,*

1INRA Rennes, UMR INRA-Agrocampus BiO3P, BP 35327, F-35653 Le Rheu Cedex
2INRA, URGI - Genoplante Info, Infobiogen, 523 place des Terrasses, F-91000 Evry, France
3CNRS INIST, 2, allée du Parc de Brabois 54500 Vandoeuvre-lès-Nancy, France

*To whom correspondence should be addressed. Denis Tagu, E-mail: denis.tagu{at}rennes.inra.fr


  Abstract

AphidBase aims to i) store recently acquired genomic resources on aphids and ii) compare them to other insect resources as functional annotation tools. For that, the Drosophila melanogaster genome has been loaded in the database using the GMOD open source softwares for a comparison with the 17,069 pea aphid unique transcripts (contigs) and the 13,639 gene transcripts of the Anopheles gambiae. Links to FlyBase and A. gambiae Entrez databases allow a rapid characterization of the putative functions of the aphid sequences. D. melanogaster literature text mining was performed to construct a network of co-cited gene or protein names which should facilitate functional annotation of aphid homolog sequences. AphidBase represents one of the first genomic databases for a Hemipteran insect.

Availability: http://w3.rennes.inra.fr/AphidBase

Associate Editor: Alvis Brazma

Received on October 13, 2006; revised on October 13, 2006; accepted on January 5, 2007

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