GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

S. Auborg, V. Brunaud, C. Bruyere, M. Cock, R. Cooke, A. Cottet, A. Couloux, P. Dehais, G. Deleage, A. Duclert, M. Echeverria, A. Eschbach, D. Falconet, G. Filippi, C. Gaspin, C. Geourjon, J-M. Grienenberger, G. Houlne, E. Jamet, F. LechauveO. Leleu, P. Leroy, R. Mache, C. Meyer, H. Nedjari, I. Negrutiu, V. Orsini, E. Peyretaillade, C. Pommier, J. Raes, J-L. Risler, S. Riviere, S. Rombauts, P. Rouze, M. Schneider, P. Schwob, Ian Small, G. Soumayet-Kampetenga, D. Stankovski, C. Toffano, M. Tognolli, M. Caboche, A. Lecharny

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Abstract

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.
Original languageEnglish
Pages (from-to)D641-D646
JournalNucleic Acids Research
Volume33
Issue numberDatabase issue
DOIs
Publication statusPublished - 2005

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Auborg, S., Brunaud, V., Bruyere, C., Cock, M., Cooke, R., Cottet, A., ... Lecharny, A. (2005). GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. Nucleic Acids Research, 33(Database issue), D641-D646. https://doi.org/10.1093/nar/gki115