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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Genome annotation in plants and fungi: EuGène as a model platform
Current Bioinformatics, Volume 3, No. 2, Year 2008
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Description
In this era of whole genome sequencing, reliable genome annotations (identification of functional regions) are the cornerstones for many subsequent analyses. Not only is careful annotation important for studying the gene and gene family content of a genome and its host, but also for wide-scale transcriptome and proteome analyses attempting to describe a certain biological process or to get a global picture of a cell's behavior. Although the number of sequenced genomes is increasing thanks to the application of new technologies, genome-wide analyses will critically depend on the quality of the genome annotations. However, the annotation process is more complicated in the plant field than in the animal field because of the limited funding that leads to much fewer experimental data and less annotation expertise. This situation calls for highly automated annotation platforms that can make the best use of all available data, experimental or not. We discuss how the gene prediction (the process of predicting protein gene structures in genomic sequences) research field increasingly shifts from methods that typically exploited one or two types of data to more integrative approaches that simultaneously deal with various experimental, statistical, or other in silico evidence. We illustrate the importance of inte-grative approaches for producing high-quality automatic annotations of genomes of plants and algae as well as of fungi that live in close association with plants using the platform EuGène as an example. © 2008 Bentham Science Publishers Ltd.
Authors & Co-Authors
Foissac, Sylvain
Spain, Barcelona
Parc de Recerca Biomèdica de Barcelona
France, Castanet-tolosan
Laboratoire de Recherche en Sciences Végétales
Gouzy, Jérõme
France, Castanet-tolosan
Laboratoire Des Interactions Plantes - Micro-organismes - Lipm
Rombauts, Stéphane
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Mathé, Catherine
France, Castanet-tolosan
Laboratoire de Recherche en Sciences Végétales
Amselem, Joëlle
France, Versailles
Centre de Recherche Île-de-france - Versailles-grignon
France, Paris
Biologie et Gestion Des Risques en Agriculture
Sterck, Lieven
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Van de Peer, Y.
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Rouzé, Pierre
Belgium, Ghent
Universiteit Gent
Schiex, Thomas
France, Castanet-tolosan
Inrae Occitanie-toulouse Centre
Statistics
Citations: 76
Authors: 9
Affiliations: 8
Identifiers
Doi:
10.2174/157489308784340702
ISSN:
15748936
Research Areas
Genetics And Genomics