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Laboratory of Plant-Microbe Interactions - LIPM

Laboratory of Plant-Microbe Interactions

Activities

The activity of the team is organized in three main topics focusing on sequence analysis. The topics are i) Genome annotation to interpret sequence data ii) Comparative genomics to transfer knowledge between species iii) Integrative web-portals to integrate bioinformatics resources in order to provide biologists with unified user interfaces.
Our primary goal is to provide our collaborators either in the lab or in other INRA/CNRS laboratories with bioinformatics tools permitting an efficient and fast exploitation of molecular data.

Genome annotation

During the last five years, we have extended tools and skills in the field of gene finding (EuGène and FrameD/FrameDP projects) as well as in the domain of functional annotation (iANT project). More recently, we have initiated the development of an annotation platform to manage the detection, clustering and annotation of ncRNAs and smallRNAs (LeARN/smallA projects). Our aim in investigating the smallRNA world was to complement our set of tools for analysing genomes and to develop new skills in the analysis of those key actors.

Collaboration: Thomas Schiex (Unité de Biométrie et d'Intelligence Artificielle - INRA Toulouse)

Comparative genomics

As one key for analyzing genome content is the comparison with other genomes, the analysis genome-by-genome can be considered as outdated. We made this assumption five years ago and this was the starting point for the development of the NARCISSE platform. Now, NARCISSE provides the users with up-to-date genome comparisons that can be browsed using various representations (dotplot, circos, karyotype, comparative maps). Quantitative data can be uploaded and duplications analysed.

Collaboration: Thomas Faraut (Laboratoire de Génétique Cellulaire - INRA Toulouse)

Integrative portals

The integration of numerous and heterogeneous produced data represents a challenge that needs to be overcome to fully exploit the considerable investment and progress made by many laboratories worldwide. Our goal is to provide and to ensure the interoperability of bioinformatics resources that are required to integrate and interpret such data. Several thematic web-portals have been developed (e.g: LEGOO for legumes and HELIAGENE for sunflower). The portals are based on the protocol BioMoby both to permit the interoperability between the different resources and to make available data and software within the bioinformatics community. The portals provide a unified entry point to numerous bioinformatics resources including a knowledge base that represents and structures published results.