« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 Databases of homologous gene families for comparatives genomics POSTER 23 Simon Penel 1, Anne-Muriel Arigon 2, Vincent Daubin 1, Pascal Calvat 3,Stéphane Delmotte 1, Jean-François Dufayard 2, Manolo Gouy 1, Guy Perrière 1, Anne-Sophie Sertier 1, Laurent Duret 1 1. Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard Lyon1, Villeurbanne 2. Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, Montpellier 3. Centre de Calcul de l’Institut National de Physique Nucléaire et de Physique des Particules /CNRS, Villeurbanne

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 Homologous gene family databases: Answers to which questions?  Select all the orthologous genes between two peculiar taxa.  Identification of good phylogenetic markers  Which are the potential gene transfers in a peculiar bacterial phylum?  How many massive duplications occured in a peculiar phylum?  Do duplicated genes evolve faster? ...

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 Homologous gene family databases: Methods ? Interest ? Pipeline: 1 selection of a set of protein sequences : all sequences of vertebrata in UniProt (HOVERGEN) complete animal genomes from Ensembl (HOMOLENS) complete genomes of selected eukaryotes, all complete genomes of bacteria and archaea (HOGENOM) complete genomes of selected eukaryotes, all complete genomes of bacteria and viruses (PhEVER) 2 similarity search (BLAST all vs all) 3 clustering of sequences into families 4 calculation of a phylogenetic tree for each family, detection of duplications Main interest of these methods : - Detection of orthology relies on phylogeny, which is more reliable than Reciprocal Best Hits - More informative than simple presence of absence of the gene

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 all vertebrate genes complete genomes archaea complete genomes animals Ensembl complete genomes viruses complete genomes bacteria Various homologous gene family databases: Various taxonomic domains complete genomes other eukaryotes all vertebrate genes

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 all vertebrate genes Various homologous gene family databases: Various taxonomic domains HOVERGEN

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 complete genomes animals Ensembl Various homologous gene family databases: Various taxonomic domains HOMOLENS

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 complete genomes archaea complete genomes animals Ensembl complete genomes bacteria Various homologous gene family databases: Various taxonomic domains complete genomes various eukaryotes HOGENOM

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 complete genomes animals Ensembl complete genomes viruses complete genomes bacteria Various homologous gene family databases: Various taxonomic domains PhEVER

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 HOGENOM (2003- today) 513 complete genomes (bacteria, archaea, some eukarya) 2,000,000 sequences PhEVER (2009-today) 2052 viruses 437 bacteria 1 human, 2 mosquitos restricted to families containing viral sequences HOVERGEN (1994-today) >20,000 vertebrata 400,000 sequences HOMOLENS(2005-today) 40 complete animal genomes 700,000 sequences Distance tree of homologous gene family databases « Evolution of vertebrata » « Viral evolution » « Genome evolution, Animal evolution » « Genome evolution, Gene transfers, Phylogeny of bacteria, Tree of life »

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 HOBACGEN  ( ) HOBACGEN -CG  ( ) 2003 HOGENOM (2003-today) PhEVER (2009-today) 2009 HOVERGEN (1994-today) HOMOLENS(2005-today) 2005 RTKdb  NUREBASE lateral transfer Phylogeny of homologous gene family databases

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 Access to homologous gene family databases

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 Access to homologous gene family databases FamFetch -TreePattern

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 Access to homologous gene family databases Acces via sockets « Query » application SeqinR (R package), Python

« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009 For more information on homologous gene family databases please visit posters: Poster 23 ”Databases of homolougous gene families for comparative genomics” and also Poster 4 ”PhEVER Phylogenetic Exploration of Viruses' Evolutionary Relationships” Leonor Palmeira