PRABI
Rhone-Alpes Bioinformatics Center
GeM is a comparative mapping database dedicated to all vertebrate complete genome including SNP (Single Nucleotide Poymorphism) data detected from ESTs (Expressed Sequence Tags).
The GeM (Genomic Mapping) project was initiated to provide a bioinformatic environment devoted to the comparative mapping management and analysis of vertebrate genomes. Thanks to the high level of genome organisation conservation between close organisms, comparative mapping is a powerful approach to study genome organisation, functioning and evolution.
The GeMCore knowledge base was developed around an original UML (Unified Modeling Langage) ’object-association’ model that formalise the complexity and the heterogeneity of comparative genomic concepts and data. The model was implemented by using PostgreSQL in a kind of data warehousing system and was updated with comparative mapping data for 9 vertebrate genomes. Access to the knowledge base can be made through the GeM web site that was designed to present the GeM architecture and to provide tools devoted to the comparative mapping of multiple organisms.
The GeMCore knowledge base was applied to manage vertebrate exonic SniPs (Single Nucleotide Polymorphisms) obtained by in-silico mining of ESTs (Expressed Sequence Tags) data processed by using the DigiPINS (Digital SniPs) pipeline. The DigiPINS web interface allows users to analyse exonic SniPS in 6 vertebrate genomes by using many comparative genomic criteria and to search for human exonic SniPS associated to cancer phenotype.
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