Analyse de données de séquençage NGS

GDEC

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Génétique, Diversité et Ecophysiologie des Céréales
Adresse

France

Téléphone
+33 (0)4 73 62 43 21
Fax
+33 (0)4 73 62 44 53
Description (English)

GDEC Team involved in Bioinformatics

English keywords
Genetic & physical & transcriptomic mapping,positional clonage,genetic recombination,genome sequencing,structural and functional annotation,workflow TriAnnot, wheat, Triticum aestivum
SFBI
Membre de la SFBI

SaAB

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Statistiques et Algorithmique pour la Biologie
Adresse

Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT)
Inra
Chemin de Borde Rouge
BP 52627

31326 CASTANET-TOLOSAN cedex

France

Téléphone
0561285074
Fax
0561285335
Description (English)

The team develops mathematical, statistical and computational methods to address life science research problems. These methods are usually directly made available to biologists through dedicated software.

Bioinformatics problems addressed

The topics addressed in the team concern the localization and identification of functional elements in bacterial, plant and animal genomes. Three investigation levels are considered.     

  • Genetical level A genome is essentially seen through molecular markers whose locations on a chromosome are highly informative in genetics investigation. Localizing these markers on the chromosomes (genetic mapping and radiated hybrid mapping: Carthagène) in order to subsequently locate the regions linked to quantitative traits of interest (disease resistance, yield ...) with respect to those markers (QTL or quantitative trait loci localization by analyzing allelic transmission: MCQTL and by modelling linkage disequilibrium: HAPim). These QTLs can then be used in selecting varieties that combine several desirable traits.
  • Molecular level At the molecular level, the DNA sequence of the genome is directly analyzed to decode and identify functional regions in the sequence. These may be genes coding for proteins (in bacterial genomes and EST cclusters FrameD or in eukaryotic genomes: EuGène) or non coding genes corresponding to functional RNAs (MilPat, DARN!, ApolloRNA, RNAspace). The comparison of genomes of different species and identification of key events that separate them (recombination) can enable the transfer of information between genomes.
  • Gene expression level The use of DNA microarrays allows to partially observe the cellular activity at a given time. It is then possible to establish a link between the contextual conditions of the cell at observation time (disease, polluted environment) and the genes that are over (or under) expressed. This link may help trace the genes related to disease or allow for a diagnosis.

To go beyond the localization of isolated functional elements, we are are now increasingly interested in approaches aiming at the inference of gene regulatory networks. We are currently studying the simultaneous analysis of expression data and polymorphism data (such as SNP) on a collection of individuals. This allows to observe different perturbated modes of operation of the network to better infer gene network structures.

English keywords
genetical and radiated hybrids mapping, QTL mapping, sequence annotation, ncRNA search, inference of gene regulatory network
SFBI
Membre de la SFBI

Bioversity International

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Bioversity International
Adresse

Bioversity International
1990 Boulevard de la Lironde
Parc Scientifique Agropolis II

34397 Montpellier

France

Téléphone
(33)467611302
Fax
(33)467610334
Description (English)

With the launch of Bioversity International, the International Network for the Improvement of Banana and Plantain (INIBAP) ceases to exist as an organization (except as a legal entity in France, its host country) but becomes instead the network of collections, curators and information scientists whose responsibility it is to take care of the world’s genetic resources of banana.

The foundation of this network is thus provided by the genebank of the INIBAP Transit Centre in Leuven, Belgium, where the greater part of the banana genepool is held, in trust for humanity, in a tissue culture collection that serves as a ‘safety back-up’ for all the diversity of banana plants growing in field collections, farms and forests around the world. A further safety back-up is provided by a steadily increasing collection of accessions that is held for the long term, without deterioration, by ‘cryopreservation’ in liquid nitrogen.

Regional and national collections around the world serve as field genebanks, holding banana varieties as growing plants, which can be used by banana breeders to make new crosses or multiplied and distributed to farmers in support of banana production. A unified information system is provided by the Musa Germplasm Information System that brings together a wealth of information on the bananas held in collections worldwide, helping users to identify and source the exact kinds of banana they need for their particular purposes. A Taxonomic Advisory Group, bringing together banana taxonomists, molecular scientists, curators and breeders, provides guidance and technical support for clarifying issues of nomenclature and developing strategies for rationalising conservation efforts.

The activities of the network are guided by the Global Conservation Strategy for Musa, which has been developed within the framework of the CGIAR/FAO Global Crop Diversity Trust, and continues to evolve in consultation with partners and in response to the needs of the banana research-and-development community.

English keywords
phylogeny, crops, banana, genome
SFBI
Membre de la SFBI