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Research in genomics involves the study of large gene sets and thus the storage, organization and analysis of huge data sets with variable origins and quality. The experimental approaches used to understand the biological functions of plant genes are numerous and complementary: genetic and physical mapping, transcriptome and proteome studies, full-length cDNA and EST sequencing, insertion mutants... The genomes of the model plants are used as physical references to gather and merge all the generated information and therefore to optimize functional predictions. Indeed, the biological interpretation of large quantities of data requires their integration, organization and visual representation. Organizing the data around the chromosome sequences allows one to reduce the redundancy of the information and references, but also to easily study the concepts of synteny and genome evolution and the relationships between the structure and the function of the genes. It is only with this general overview that the functional study of genes and the orthology quest will be possible, taking into account patterns of regulation and roles and relationships of genes in particular physiological states. Therefore, the ultimate objective of this project is to develop a database and associated bioinformatics tools based on the integration of genomic data around a selection of plant complete genomes. This tool will help users to understand the biological role of plant genes by considering them in a wide context: a multigene family, a topological environment, and/or a functional network. The database and the associated user-friendly interface (in Java JDK1.4) is developed with a conceptual effort for the graphical display and the hierarchical organization of the data. The running integration involves the structural and functional international annotations, EST from different plant species, novel gene predictions, mutant tags, gene families, protein motifs, transcriptome data, repeat sequences, primers and tags for genomic approaches (DNA chips, synteny studies, BAC library screening, RT-PCR, SNP discovery, ...), subcellular targeting, secondary structures, 3D models, MPSS tags, curated annotations and mutant phenotypes.

Genomes present in FLAGdb⁺⁺ :

Arabidopsis thaliana (Columbia 0)

Oryza sativa (spp japonica cv.Nipponbare)

Vitis vinifera (PN40024)

Populus trichocarpa (Nisqually-1 clone)