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Genome annotation in plants and fungi: EuGène as a model platform

(2008) CURRENT BIOINFORMATICS. 3(2). p.87-97
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Abstract
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 integrative 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 EuGene as an example.
Keywords
SEQUENCES, IDENTIFICATION, DATA-SET, EUKARYOTES, INTEGRATION, SPLICE SITES, ARABIDOPSIS GENOME, PRE-MESSENGER-RNA, HIDDEN MARKOV MODEL, GENE STRUCTURE PREDICTION, gene finding, plants, genome annotation, fungi

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MLA
Foissac, Sylvain, Jérôme Gouzy, Stephane Rombauts, et al. “Genome Annotation in Plants and Fungi: EuGène as a Model Platform.” CURRENT BIOINFORMATICS 3.2 (2008): 87–97. Print.
APA
Foissac, S., Gouzy, J., Rombauts, S., Mathé, C., Amselem, J., Sterck, L., Van de Peer, Y., et al. (2008). Genome annotation in plants and fungi: EuGène as a model platform. CURRENT BIOINFORMATICS, 3(2), 87–97.
Chicago author-date
Foissac, Sylvain, Jérôme Gouzy, Stephane Rombauts, Catherine Mathé, Joëlle Amselem, Lieven Sterck, Yves Van de Peer, Pierre Rouzé, and Thomas Schiex. 2008. “Genome Annotation in Plants and Fungi: EuGène as a Model Platform.” Current Bioinformatics 3 (2): 87–97.
Chicago author-date (all authors)
Foissac, Sylvain, Jérôme Gouzy, Stephane Rombauts, Catherine Mathé, Joëlle Amselem, Lieven Sterck, Yves Van de Peer, Pierre Rouzé, and Thomas Schiex. 2008. “Genome Annotation in Plants and Fungi: EuGène as a Model Platform.” Current Bioinformatics 3 (2): 87–97.
Vancouver
1.
Foissac S, Gouzy J, Rombauts S, Mathé C, Amselem J, Sterck L, et al. Genome annotation in plants and fungi: EuGène as a model platform. CURRENT BIOINFORMATICS. 2008;3(2):87–97.
IEEE
[1]
S. Foissac et al., “Genome annotation in plants and fungi: EuGène as a model platform,” CURRENT BIOINFORMATICS, vol. 3, no. 2, pp. 87–97, 2008.
@article{439456,
  abstract     = {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 integrative 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 EuGene as an example.},
  author       = {Foissac, Sylvain and Gouzy, Jérôme and Rombauts, Stephane and Mathé, Catherine and Amselem, Joëlle and Sterck, Lieven and Van de Peer, Yves and Rouzé, Pierre and Schiex, Thomas},
  issn         = {1574-8936},
  journal      = {CURRENT BIOINFORMATICS},
  keywords     = {SEQUENCES,IDENTIFICATION,DATA-SET,EUKARYOTES,INTEGRATION,SPLICE SITES,ARABIDOPSIS GENOME,PRE-MESSENGER-RNA,HIDDEN MARKOV MODEL,GENE STRUCTURE PREDICTION,gene finding,plants,genome annotation,fungi},
  language     = {eng},
  number       = {2},
  pages        = {87--97},
  title        = {Genome annotation in plants and fungi: EuGène as a model platform},
  url          = {http://dx.doi.org/10.2174/157489308784340702},
  volume       = {3},
  year         = {2008},
}

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