2011
Plant & Animal Genomes XIX Conference, January 15-19, 2011, San Diego, CA
15 Jan 2011 Genome Annotation And Report System: An Integrated System For Structural And Functional Genome AnnotationAmselem J, Alaux M, Brault B, Lapalu N, Legeai F, Alfama F, Brigitte L, Choisne N, Keliet A, Kimmel E, Kreplak J, Luyten I Pommier C Reboux S, SIDIBE BOCS S, Steinbach D, Lebrun MH, Quesneville H
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 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.
Creation date: 12 Jan 2011
eZ PublishPublication supervisor: A-F. Adam-Blondon
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