Databases of homologous gene families
Comparison of homologous sequences is an essential step for many studies related to molecular biology and evolution. To simplify the search for homologues, the Helix research group at Lyon have developed several databases of gene families: HOVERGEN (vertebrates), HOBACGEN (prokaryotic organisms) and HOGENOM (completely sequenced genomes).
We also have developed some specialized databases, dedicated to complex gene families: NuRebase (nuclear receptors) and RTKdb (receptor tyrosine kinase). In these databases, homologous protein genes are classified into families, and for each family a multiple alignment and a phylogenetic tree are computed. All these data can be accessed through a webserver or via a dedicated graphical interface (FamFetch).
New algorithms have been developed for the reconciliation of species and gene trees, and for the search for tree patterns in a collection of phylogenetic trees. These algorithms have been implemented in FamFetch and allow the automatic retrieval of orthologs and paralogs in our databases of gene families.
Software development for molecular phylogeny
We are developing a client-server application for molecular phylogeny: PhyloJava. The main features of PhyloJava are:
user-friendly graphical interface for the management of alignments and phylogenetic trees
public access to a large range of methods, available on remote servers
Molecular phylogeny of prokaryotes and eukaryotes
Phylogenetic relationships between very distantly related organisms are difficult to establish. We have taken advantage of the availability of complete genome sequences to build the phylogenetic tree of archaea and bacteria, by using a supertree method. We notably have shown that there exists a core of genes sharing a common history and hence that can be used to infer a tree. This phylogeny presents several differences with the rRNA phylogeny, notably for the position of hyperthermophilic bacteria.
Horizontal gene transfers
Horizontal transfers of genes between different species seem to be relatively common in bacteria and archea. However, the origin of these laterally transferred genes remains obscure. We are working on the detection and analysis of lateral gene transfers. We have notably shown that most observed lateral gene transfers do not correspond to free exchange of regular genes among bacterial genomes, but more probably represent the constituents of phages or other selfish elements.