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2011

International,  COM (talks)

Botrytis-Sclerotinia Post-Genome Workshop 15th- 17th September 2011 – Lyon, FRANCE

17 Sep 2011   Botrytis/Sclerotinia resources: an integrated system for structural and functional genome annotation

  Joelle Amselem , Nicolas Lapalu , Baptiste Brault, Laetitia Brigitte, Jonathan Kreplak, Françoise Alfama, Aminah Keliet, Erik Kimmel, Isabelle Luyten, Sébastien Reboux, Delphine Steinbach, Marc-Henri Lebrun and Hadi Quesneville

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 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 or set up at URGI to make available to the community, data provided by structural annotation (B. cinerea T4) and functional annotation (B. cinerea T4, B0510 and S. sclerotiorum) :

- 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.

- A synteny browser has also been set up for B. cinerea T4, B0510 and S. sclerotiorum

- 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 (GRS edition) to allow manual functional annotation.

 - Quick and advanced search are processed respectively through GnpIS QuickSearch and Biomart (GMOD).

We will present all these resources in the frame of Botrytis/Sclerotinia genome project.


Keywords: talk BSPGW Botrytis Sclerotinia Workshop
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Update: 12 Aug 2015
Creation date: 20 Sep 2011