Author Archive

WP4

Posted on octobre 7, 2010 by Commentaires fermés sur WP4

Phylogeny and Comparative Genomics

ReNaBi’s platforms are developing algorithms for phylogenetic reconstruction (e.g. PhyML, Guindon et al. 2010) and tools for analyzing and viewing trees (e.g. TreeDyn or NJplot). These works are implemented in software applications that we distribute on the web; they may be downloaded and/or executed on-line. We also design integrated pipelines to compute multiple alignments, build trees and view the results in a user friendly environment (SeaView program, Gouy et al. 2010, and http://www.Phylogeny.fr/ web server, Dereeper et al. 2008). These programs and services are highly cited (PhyML >3,000 since original publication in 2003, SeaView >1,000 since original publication in 1996, cf. Web of Science) and widely used worldwide (Phylogeny.fr 10,000 analyses per month).
We are also working out phylo and comparative genomic databases, which are outstanding resources to elucidate the evolution and function of genes. HOVERGEN, HOGENOM and HOMOLENS (Penel et al. 2009, http://www.prabi.fr/) contain protein gene sequences clustered into groups of homologs. They integrate multiple sequence alignments and phylogenetic trees, and are regularly used for evolutionary studies (> 250 citations). GREENPHYLDB (Rouard et al. 2010) contains plant multigenic families and their associated orthology relationships derived from phylogenetic analyses. SOUTHGREEN provides a large panel of tools to analyze the genomes of tropical agronomy plants. All these databases are widely accessed (SOUTHGREEN 50,000 accesses per month, http://southgreen.cirad.fr/).

Filed Under: Supplemental-material

ReNaBi – Grand SudReNaBi – Grand Sud

Posted on septembre 25, 2010 by Commentaires fermés sur ReNaBi – Grand SudReNaBi – Grand Sud

The ReNaBi-Grand Sud  regional center currently gathers four PFs located in the South part of France (IGS Marseille, CAZy Marseille, IMGT Montpellier, and ATGC Montpellier, Nice and Perpignan) with a staff of 42 people.

  • ATGCbioinformatics platform involves several teams:
    • CRBM (Montpellier)
    • GET (Montpellier)
    • IPMC (Nice)
    • IRD (Montpellier)
    • LGDP (Perpignan)
    • LIRMM (Montpellier)
    • South Green (Montpellier)
  • CAZy
  • IGS
  • IMGT

Biological models and applications

Each PF possesses its own specificity: ATGC covers evolutionary, comparative and functional genomics with an emphasis on algorithmics and software developments, and applications to tropical plants; CAZy attempts to cover all carbohydrate-active enzymes across all sequenced genomes; IMGT is the global reference in immunogenetics and immunoinformatics; IGS covers functional and structural genomics, with emphasis on intracellular pathogens and viruses. ReNaBi-GS thus has expertise in a large spectrum of fields, including Health, Agronomy, Evolution, and Ecology.

Databases and software tools

ATGC and IGS provide the community with original software tools, some widely used and cited. All PFs provide specialized databases, some being the international reference in their domain (e.g. IMGT, CAZy, or SouthGreen for the genomics of tropical plants). ReNaBi-GS is involved in many collaborative projects with biologists, e.g. from marine ecology (IGS) or the genomics of major pathogens such as Plasmodiums and Leishmania (ATGC). Our aim is to push forward existing methods and develop bioinformatics tools and databases with high international impact.

Project support and training

The ReNaBi-GS engineers can take care of different projects or requests from the biologist community, according to their area of expertise. For example, we help users to treat the millions of reads that are obtained through new generation sequencing, thanks to original programs and our computing facilities. We participate to the GRISBI project to share the computing resources with other ReNaBi nodes. We train students in various masters of bioinformatics, both at Montpellier and Marseille, and organize training sessions (e.g. on phylogeny) and regular bioinformatics seminars.

Indicators

ReNaBi-GS services are internationally renowned and used worldwide. Some of our computer programs are highly cited (e.g.  PhyML and T-Coffee, with 3,000 and 2,000 citations, respectively, cf. Web of Science) and our databases are widely accessed (e.g. IMGT, CAZy and SouthGreen, with 150,000, 150,000 and 50,000 requests per month, respectively).

Filed Under: Platforms