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Bioinformatics Advance Access originally published online on January 19, 2007
Bioinformatics 2007 23(6):783-784; 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, Agrocampus Rennes, UMR 1099 BiO3P (Biology of Organisms and Populations applied to Plant Protection), F-35653 LE RHEU, France, 2INRA, URGI - Genoplante Info, Infobiogen, 523 place des Terrasses, F-91000 Evry, France and 3CNRS INIST, 2, allée du Parc de Brabois 54500 Vandoeuvre-lès-Nancy, France

*To whom correspondence should be addressed.


  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 software 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. Text mining of the D.melanogaster literature 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

Contact: denis.tagu{at}rennes.inra.fr, jean-pierre.gauthier{at}rennes.infra.fr

Associate Editor: Alvis Brazma

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

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