URGI plant and fungi platform: distributed resources through GMOD tools

Abstract

International audienceNext Generation Sequencing technologies produce very large amount of data. Indeed, genomes are (re-)sequenced at high pace, and new sequences data are produced (eg. RNA-seq, Chip-seq). To face this challenge, the URGI ( http://urgi.versailles.inra.fr ) platform aims at providing tools for genomics, genetics, transcriptomics and polymorphisms comprising: pipelines, databases and user-friendly interfaces to analyze, browse and query the data. We will present plant and fungal genomic resources distributed through GMOD tools integrated in our Information System GnpIS.- Our genome module database (DB) components rely on the well-known schemas from the GMOD consortium. All annotation features and analysis results are primarily stored in the Chado or Bio::SeqFeature schema according to the need. Data can then be searched through GnpIS QuickSearch based on Apache Lucene™. Indexes are generated to query data stored in same or separate GMOD DBs. Query results are returned according to significance with terms, and linked to other GnpIS modules and/or Genome Report System (GRS). Biomart (GMOD) based datamarts were used as an advance search tool. Results of complex search criteria could be exported in different formats or directly send to our Galaxy server for further bioinformatic analysis.- We provide textual or graphical interfaces over the DBs such as GBrowse or Gbrowse_Syn to display sequence annotations or synteny respectively and Apollo for genes structure curation. The GRS provides comprehensive categories of reports through a user-friendly textual interface over structural and functional genomic data stored in Chado databases. - We also present the pipelines we developed for differential gene expression and polymorphism analysis available through our Galaxy server