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« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009
Databases of homologous gene families
for comparatives genomicsPOSTER 23
Simon Penel 1, Anne-Muriel Arigon2, Vincent Daubin1, Pascal Calvat 3,Stéphane Delmotte1,
Jean-François Dufayard2, Manolo Gouy 1, Guy Perrière 1, Anne-Sophie Sertier1, Laurent Duret1
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 families4 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 genomesarchaea
complete genomesanimalsEnsembl
complete genomesviruses
complete genomesbacteria
Various homologous gene family databases:
Various taxonomic domains
complete genomesother 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 genomesanimalsEnsembl
Various homologous gene family databases:
Various taxonomic domains HOMOLENS
« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009
complete genomesarchaea
complete genomesanimalsEnsembl
complete genomes bacteria
Various homologous gene family databases:
Various taxonomic domains
complete genomesvarious eukaryotes
HOGENOM
« Databases of homologous gene families for comparatives genomics » Poster 23 - JOBIM Nantes - Juin 2009
complete genomesanimalsEnsembl
complete genomesviruses
complete genomesbacteria
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 viruses437 bacteria1 human, 2 mosquitosrestricted to families containing viral sequences
HOVERGEN (1994-today)>20,000 vertebrata400,000 sequences
HOMOLENS(2005-today)40 complete animal genomes700,000 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 (1997-2000)
1997
1994
HOBACGEN -CG (2000-2004)
2003
HOGENOM (2003-today)PhEVER (2009-today)
2009
HOVERGEN (1994-today)HOMOLENS(2005-today)
2005RTKdb
NUREBASE
20012002
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
http://pbil.univ-lyon1.fr
« 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