« databases of homologous gene families for comparatives genomics » poster 23 - jobim nantes -...

« 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


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?

...


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


all vertebrate genes

complete genomesarchaea

complete genomesanimalsEnsembl

complete genomesviruses

complete genomesbacteria

Various homologous gene family databases:

Various taxonomic domains

complete genomesother eukaryotes





Various taxonomic domains HOVERGEN




Various taxonomic domains HOMOLENS


complete genomesarchaea


complete genomes bacteria



complete genomesvarious eukaryotes

HOGENOM



complete genomesviruses

complete genomesbacteria



PhEVER


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 »


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


Access to homologous gene family databases

http://pbil.univ-lyon1.fr



FamFetch -TreePattern



Acces via sockets« Query » application

SeqinR (R package), Python


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

« databases of homologous gene families for comparatives genomics » poster 23 - jobim nantes -...

Documents

potential gene transfers

complete genomes of

phylogenetic tree

phylogeny of bacteria

peculiar phylum

physique nuclaire et

tree of lifephylogeny

robotique et