Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

The MIPS Plant Genome Analysis And Database Framework

Manuel Spannagl , Octave Noubibou , Heidrun Gundlach , Tobias Hindemitt , Kathrin Klee , Georg Haberer , Klaus FX Mayer

  MIPS, Institute for Bioinformatics, GSF Research Center for Environment and Health, Ingolstädter Landstr. 1 85764 Neuherberg, Germany

Genome-oriented plant research delivers rapidly increasing amount of plant genome data. Comprehensive and structured information resources are required to structure and communicate genome and associated analytical data for model organisms as well as for crops. The increase in available plant genomic data enables powerful comparative analysis and integrative approaches. We have developed MIPS PlantsDB that aims to provide data and information resources for individual plant species and in addition to build a platform for integrative and comparative plant genome research. PlantsDB aims to address this task by applying a generic though highly flexible modular database infrastructure for a wide range of plant genomic data. PlantsDB is constituted from genome databases for Arabidopsis, Medicago, Lotus, rice, maize and tomato. Complementary data resources for cis elements, repetive elements and extensive cross-species comparisons are implemented. The respective species databases are updated and new data are continuously integrated either through adjustment against external resources or via the groups participation in a range of plant genome sequencing projects. Topic of the presentation will be an overview of available services and specific features like the SIMAP (similarity matrix of proteins) database.
Important components within the modular and highly flexible analytical machinery circumvent standard components like e.g. structural genome annotation. However, increasing focus is devoted to non-coding fraction of plant genomes and tools and analysis for the analysis and classification of e.g. repeat elements and cis elements have been developed and applied. We will introduce individual tools, strategies and approaches we developed for the automated analysis of the nested structure of transposable elements and the detection of cis elements through comparative and integrative means. Approaches, results and biological implication will be discussed in the context of current plant genome sequencing projects.