Databases of homologous gene families: new developments and web interfaces. Equipe Bioinformatique et Génomique Evolutive Laboratoire de Biométrie et Biologie Evolutive Université Claude Bernard - Lyon 1 Simon Penel, Julien Grassot, Laurent Duret, Manolo Gouy, Guy Perrière. Pôle Bio-Informatique Lyonnais
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Databases of homologous gene families: new developments and web interfaces. Equipe Bioinformatique et Génomique Evolutive Laboratoire de Biométrie et Biologie.
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Databases of homologous gene families: new developments and web interfaces.
Equipe Bioinformatique et Génomique Evolutive
Laboratoire de Biométrie et Biologie EvolutiveUniversité Claude Bernard - Lyon 1
Simon Penel, Julien Grassot, Laurent Duret, Manolo Gouy, Guy Perrière.
Pôle Bio-Informatique Lyonnais
Homologous Genes Databases
Research fields:• Proteome/genome comparative analysis• Phylogenetic studies• Orthology/Paralogy relationship assignments• Development of generalist databases, specialised databases
– HOVERGEN: families of homologous vertebrate genes– HOBACGEN: families of homologous bacterial genes– NureBase, RTKdb, Hoppsigen, Mitalib,..
Important regions identification in genomic sequencesEvolution at the molecular levelSpecies phylogenyFunction prediction
Extension of HOVERGEN and HOBACGEN to all organisms for which the complete genome sequence has
been determined• Structured under the ACNUC (M. Gouy) retrieval system: flat file & index
files
• Integrates :
– Protein multiple alignments
– Phylogenetic trees
– Taxonomic data
– Nucleic and protein sequences
– Sequence annotations
The HoGenom database:Homologous Genes Families of
fully Sequenced OrganismsEuropean project TEMBLOR
Building of HoGenomSelection of fully sequenced organisms protein
sequences on the EBI proteome site.
Sequence comparison with BLAST on the whole sequences dataset
Clustering of the sequences in genes family on the basis of sequence similarity (transitive
association)
Add the gene family info in the protein sequence annotations