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

Sébastien Aubourg UGent, Véronique Brunaud, Clémence Bruyère, Mark Cock, Richard Cooke, Annick Cottet, Arnaud Couloux, Patrice Déhais UGent, Gilbert Deléage and Aymeric Duclert, et al. (2005) NUCLEIC ACIDS RESEARCH. 33(suppl. 1). p.D641-D646
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
MODEL, INFORMATION, UNIPROT, GENOME ANNOTATION, SECONDARY STRUCTURE PREDICTION, DATABASE, SEQUENCES, THALIANA, KNOWLEDGEBASE, IDENTIFICATION
journal title
NUCLEIC ACIDS RESEARCH
Nucleic Acids Res.
volume
33
issue
suppl. 1
pages
D641 - D646
Web of Science type
Article
Web of Science id
000226524300132
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
7.552 (2005)
JCR rank
24/256 (2005)
JCR quartile
1 (2005)
ISSN
0305-1048
DOI
10.1093/nar/gki115
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
331343
handle
http://hdl.handle.net/1854/LU-331343
date created
2006-04-14 13:36:00
date last changed
2013-10-11 11:37:08
@article{331343,
  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.},
  author       = {Aubourg, S{\'e}bastien and Brunaud, V{\'e}ronique and Bruy{\`e}re, Cl{\'e}mence and Cock, Mark and Cooke, Richard and Cottet, Annick and Couloux, Arnaud and D{\'e}hais, Patrice and Del{\'e}age, Gilbert and Duclert, Aymeric and Echeverria, Manuel and Eschbach, Aim{\'e}e and Falconet, Denis and Filippi, Ghislain and Gaspin, Christine and Geourjon, Christophe and Grienenberger, Jean-Michel and Houln{\'e}, Guy and Jamet, Elisabeth and Lechauve, Fr{\'e}d{\'e}ric and Leleu, Olivier and Leroy, Philippe and Mache, R{\'e}gis and Meyer, Christian and Nedjari, Hafed and Negrutiu, Ioan and Orsini, Val{\'e}rie and Peyretaillade, Eric and Pommier, Cyril and Raes, Jeroen and Risler, Jean-Loup and Rivi{\`e}re, St{\'e}phane and Rombauts, Stephane and Rouz{\'e}, Pierre and Schneider, Michel and Schwob, Philippe and Small, Ian and Soumayet-Kampetenga, Ghislain and Stankovski, Darko and Toffano, Claire and Tognolli, Michael and Caboche, Michel and Lecharny, Alain},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {MODEL,INFORMATION,UNIPROT,GENOME ANNOTATION,SECONDARY STRUCTURE PREDICTION,DATABASE,SEQUENCES,THALIANA,KNOWLEDGEBASE,IDENTIFICATION},
  language     = {eng},
  number       = {suppl. 1},
  pages        = {D641--D646},
  title        = {GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts},
  url          = {http://dx.doi.org/10.1093/nar/gki115},
  volume       = {33},
  year         = {2005},
}

Chicago
Aubourg, Sébastien, Véronique Brunaud, Clémence Bruyère, Mark Cock, Richard Cooke, Annick Cottet, Arnaud Couloux, et al. 2005. “GeneFarm, Structural and Functional Annotation of Arabidopsis Gene and Protein Families by a Network of Experts.” Nucleic Acids Research 33 (suppl. 1): D641–D646.
APA
Aubourg, S., Brunaud, V., Bruyère, C., Cock, M., Cooke, R., Cottet, A., Couloux, A., et al. (2005). GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. NUCLEIC ACIDS RESEARCH, 33(suppl. 1), D641–D646.
Vancouver
1.
Aubourg S, Brunaud V, Bruyère C, Cock M, Cooke R, Cottet A, et al. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. NUCLEIC ACIDS RESEARCH. 2005;33(suppl. 1):D641–D646.
MLA
Aubourg, Sébastien, Véronique Brunaud, Clémence Bruyère, et al. “GeneFarm, Structural and Functional Annotation of Arabidopsis Gene and Protein Families by a Network of Experts.” NUCLEIC ACIDS RESEARCH 33.suppl. 1 (2005): D641–D646. Print.