File:PAG2011 annotation poster JAmselem.pdf
Genome Annotation And Report System: An Integrated System For Structural And Functional Genome Annotation
Poster presented at PAG 2011.
Joelle Amselem, Michael Alaux, Baptiste Brault, Nicolas Lapalu, Fabrice Legeai, Francoise Alfama, Laetitia Brigitte, Nathalie Choisne, Aminah Keliet, Erik Kimmel, Jonathan Kreplak, Isabelle Luyten, Cyril Pommier, Sebastien Reboux, Stephanie SIDIBE BOCS, Delphine Steinbach, Marc-Henri Lebrun, Hadi Quesneville; all of INRA and CIRAD.
Nowadays with the development of NGS, more and more genomes are sequenced, producing very large amount of data. However, annotations can’t keep pace, introducing a lack between genome data and annotation releases. To face this challenge, the URGI (http://urgi.versailles.inra.fr) platform aims at providing tools to annotate entirely sequenced genome comprising: pipelines, databases and user-friendly interfaces to browse and query the data. We will focus here on complementary systems developed in the frame of GnpIS and GnpAnnot project:
- The distributed annotation system allows the curation of gene structure. This system relies on the well known GMOD databases and interfaces (Chado/GBrowse/Apollo). Curated data are available and shared by the consortium community as soon as they are committed in the database using the "pure JDBC" direct communication protocol between Apollo and Chado.
- The Genome Report System (GRS), written in Java, was developed to produce various and user-friendly Web reports. GRS uses structural and functional genomic data stored in Chado database in order to provide users with a comprehensive list of information including cross references related to a specific gene. GRS proposes also a Gene Ontology browser and an editing module (GRE) to allow manual functional annotation.
- Quick and advanced search are processed respectively through GnpIS QuickSearch (http://urgi.versailles.inra.fr/gnpis) and BioMart (GMOD).
We will present the integration of these tools in the frame of a fungal genome annotation.
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