GnpAnnot Project 2008

GnpAnnot Project 2008

Purpose

- Develop a platform of structural and functional annotation supported by comparative genomics results - Dedicated to plant and bio-aggressor genomes

- Allowing both automatic predictions and manual curation of genes and transposable elements - User-friendly, generic, modular, portable, sustainable, upgradable et compatible

Stéphanie Sidibe Bocs1_{, Gaëtan Droc}1_{, Manuel Ruiz}1 Mathieu Rouard2_{, Nicolas Roux}2

1 _{UMR DAP, CIRAD, Montpellier} 2 _{CfL, Bioversity, Montpellier}

Michael Alaux3_{, Delphine Steinbach Samson}3_{, Erik Kimmel}3_{, Cyril Pommier}3_{, Isabelle} Luyten3_{, Hadi Quesneville}3

Franck Giacomoni4_{, Philippe Leroy}4 Nancy Terrier5

3 _{URGI, INRA, Evry} 4 _{UMR GDEC, INRA, Clermont} 5 _{UMR SPO, INRA, Montpellier}

Joelle Amselem6_{, Adeline Simon}6_, Vic-toria Dominguez Del Angel6_{, Claire} Hoede6_{, Sabine Fillinger}6_{, Michel} Meyer6_{, Thierry Rouxel}6_{, Marc-Henri} Lebrun6

6 _{UMR BIOGER, INRA, Versailles}

Fabrice Legeai7_{, Jean-Pierre Gauthier}7_{, Denis Tagu}7 François Cousserans8_{, Philippe Fournier}8

7 _{UMR BIO3P, INRA, Le Rheu}

BIVI

8 _{UMR BIVI, INRA, Montpellier}

References: http://urgi.versailles.inra.fr/projects/ GnpAnnot http://genmapping.cirad.fr/genmapp ing/collaborativebioinfo/index.php http://www.gmod.org Contact: [email protected] [email protected] [email protected] [email protected]

To do

- Improve annotation systems: pipelines, parsers, roundtrips, editions, reports, queries, extractions - Integrate annotation systems: structure, function, comparison; automatic, manual; gene, TE

- Manage annotation history: automatic and manual annotation versions for a genomic sequence - Populate the different instances: monocotyledones, wheat / grapevine, fungi, insects

- Train annotators and validate the annotation tools

- Reconcile two sets of annotation for the same genomic sequence

- Manage annotation update: new manual gene structures, new genomic sequence version

Genome Browser Structural annotation Apollo Artemis Argo Comparative genomics SynBrowse SynView ACT Combo Other systems GenoStar Legoo Vista MEGA GnpIS Gene/protein Query Refinment analyses Blast Exonerate Sim4, GeneSeqer InterProscan Home platform Parser Reconciler Extractor Extractor Pipeline Pipeline Interface Web Interface Web Client Interface Web Client Interface Web Chado Model Database

API, data exchange format

Automatic Predictions EuGene RepeatMasker tRNAscan Databank Genbank/EMBL UniProt InterPro Reference Ontologies Communications Wiki Alfresco JIRA CVS

CECILL open source CiteULike

1. New genomic sequence 2. New gene annotation

3. Other gene annotation set 4. New assembly of a genomic sequence

GnpAnnot platform

Table Editor Gene/protein Report Sidibe Bocs WP5 Manual annotation platform validation Fungi Evry Amselem INRA-BIOGER Insects Rennes Legeai INRA-BIO3P INRA-BIVI Wheat/Grape Evry Alaux INRA-URGI INRA-GDEC INRA-SPO

Amselem Legeai Sidibe Bocs Alaux

WP1 WP2 WP3 WP4 DB manage ment Annotation interfaces Intero perability Communi-cation Pipeline exploitation platform release cvs wiki Sidibe Bocs Browse Query Manual annotation Analysis DB Pipeline Bank

Bioinformatics platforms (IBiSA label, ReNaBi)

Monocots Montpellier Sidibe Bocs CIRAD-DAP Bioversity CfL

GnpAnnot

management

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