Nucleic Acids Research, 2005, Vol. 33, Database issue D641-D646
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts
1 Unité de Recherche en Génomique Végétale (INRA/CNRS/UEVE) 2 Rue Gaston Crémieux, CP 5708, 91057 Evry Cedex, France, 2 Institut de Biotechnologie des Plantes (CNRS/UPS) Bâtiment 630, Université Paris-Sud, 91405 Orsay Cedex, France, 3 Station Biologique de Roscoff (CNRS/UPMC) Place Georges Tessier, BP 74, 29682 Roscoff Cedex, France, 4 Laboratoire de Physiologie et de Biologie Moléculaire des Plantes (CNRS/UP) and 5 Laboratoire Génome et Développement des Plantes (CNRS/UP), 52 Avenue de Villeneuve, Université de Perpignan, 68860 Perpignan Cedex, France, 6 Laboratoire Plastes et Différenciation Cellulaire (CNRS/UJF) Université J. Fourrier, BP 53, 38041 Grenoble Cedex 09, France, 7 Plant Systems Biology (INRA/VIB/GU) K.L. Ledeganckstraat 35, 9000 Ghent, Belgium, 8 Institut de Biologie et Chimie des Protéines (PBIL/CNRS) 7 Passage du Vercors, 69367 Lyon Cedex 7, France, 9 Unité de Recherche en Génomique-Info (INRA/GENOPLANTE) 523 Place des Terrasses, 91000 Evry, France, 10 Institut de Biologie Moléculaire des Plantes (CNRS) 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France, 11 Equipe Statistique et Informatique (INRA) Chemin de Borde Rouge, Auzeville BP 27, 31326 Castanet-Tolosan, France, 12 UMR Amélioration and Santé des Plantes (INRA/UBP) 234 Avenue du Brézet, Domaine de Crouelle, 63039 Clermont-Ferrand Cedex 2, France, 13 Laboratoire Nutrition Azotée des Plantes (INRA) Route de Saint-Cyr, 78026 Versailles Cedex, France, 14 Laboratoire de Reproduction et Développement des Plantes (INRA/CNRS/ENS/UL) 46 Allée d'Italie, Université Lyon I, 69364 Lyon Cedex 07, France, 15 Laboratoire Génome et Informatique (CNRS) 523 Place des Terrasses, 91034 Evry, France and 16 Swiss Institute of Bioinformatics (Swiss-Prot) CMU, 1 Michel Servet, CH-1211 Genève 4, Switzerland
* To whom correspondence should be addressed. Tel: +33 1 60 87 45 16; Fax: +33 1 60 87 45 49; Email: aubourg{at}evry.inra.fr
Received August 12, 2004; Revised and Accepted October 15, 2004
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.
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