WG-InferPhy : WorkGroup Inférence Phylogénétique
Fed DBGS /wikili/index.php/
Responsible : Julie Thompson
Participants : Julie Thompson
Description : The development of new strategies for automatic, reliable phylogenetic inference in large-scale projects.
The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses to understand the mechanisms involved in the evolution of the genome and their consequences in the study of biological systems. Phylogenetic approaches provide a unique conceptual framework for performing comparative analyses of all this data, for propagating information between different systems and for predicting or inferring new knowledge. As a result, phylogenetic inference systems are now playing an increasingly important role in most areas of high throughput genomics, including studies of promoters (phylogenetic footprinting), interactomes (based on the presence and degree of conservation of interacting proteins), and in comparisons of trancriptomes or proteomes (phylogenetic proximity and co-regulation/co-expression).
We are building on our past experience in the contruction and exploitation of Multiple Alignments of Complete Sequences (MACS). In the past, we have developed a number of tools aimed at constructing high quality MACS (DbClustal, RASCAL, LEON, NorMD). An important aspect is the objective evaluation of our tools based on the BAliBASE benchmark suite. This research axis is now continuing, with the development of a new alignment expert system AlexSys. More recently, we have also addressed the problems of the automatic integration of heterogeneous information in the context of a protein family alignment, with the development of a Multiple Alignment Ontology (MAO) and a new MACS-based Information Management System (MACSIMS).
All these tools are exploited in a number of different biological applications, including genome annotation and analysis (e.g. Mycobacterium Smegmatis, Alvinella Pompejana), structure/function/evolution analysis (e.g. Muscular Interactome, MyoNet), construction of evolutionary histories for the human proteome (EvolHHuPro).