Annotation of Tomato Stephane Rombauts Wageningen 18/09/2004 Bioinformatics & Evolutionary Genomics Ghent, Belgium.

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Presentation transcript:

Annotation of Tomato Stephane Rombauts Wageningen 18/09/2004 Bioinformatics & Evolutionary Genomics Ghent, Belgium

2 Contribution to the project Structural gene prediction Structural gene prediction Genome structure analyses Genome structure analyses Provide to EU-SOL-community with the genemodels as soon as ready Provide to EU-SOL-community with the genemodels as soon as ready Provide annotation tools to users Provide annotation tools to users

3 Structural annotation Involves: Involves: Build training set for software training Build training set for software training Build a tomato/solanaceae-specific EuGene platform Build a tomato/solanaceae-specific EuGene platform Identify and annotate transposable elements, as those interfere with gene prediction Identify and annotate transposable elements, as those interfere with gene prediction Predict ncRNAs (tRNAs, rRNAs, microRNAs) Predict ncRNAs (tRNAs, rRNAs, microRNAs)

4 Genome structure Analysis of whole genome structure using i-ADHoRe. Analysis of whole genome structure using i-ADHoRe. Provides overview of block duplications throughout the different available plant genomes Provides overview of block duplications throughout the different available plant genomes Will provide extensive orthologous genes between plant genomes. Will provide extensive orthologous genes between plant genomes.

5 Data display Show data through Gbrowse (= Genome annotation browser) and share it through LDAS or bioMoby Restricted access for consortium during project, World wide if OK with consortium after project completion

6 Bioinformatics & Evolutionary Genomics Eric Bonnet (miRNAs, DB, cluster administrator) Dirk Gevers (procaryotes, genome organization) Jeroen Raes (gene families, phylogeny) Carine Serizet* (Arabidopsis genome annotation) Jan Wuyts (DNA & Protein structures, miRNA) Stephane Rombauts (genome annotation, promoters, DB) Francis Dierick (web-applications, DB) genome organization Cedric Simillion Klaas Vandepoele Wouter Devos* Cindy Martens Computer scientist Sven Degroeve Yvan Saeys Guy Baele Dirk Vandycke (extrinsic annotation) Stefanie Debodt (gene families, phylogeny) Tine Casneuf (pathways & gene expression) Kobe Florquin (Promoter prediction) Lieven Sterck (poplar genome) Steven Robbens (algae genomes) Martin Kuiper (head of Computational biology) Steven Maere (pathways) Steven Vercruysse (clustering) Elena Tsiporkova Yves Van de Peer Pierre Rouze