Formulaire pour demande d' homologation cati

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1.Caractérisation de la mission du Cati : 3

2. Organisation du Cati 6

Projets Phares 15

Axe 1: Organisation et régulation des génomes 16

ANAIS: Analysis of NimbleGen Arrays Interface 17

ANATool : The Arabidopsis Natural Accession Tool 18

Base de données génomiques sur les insectes 19

19

BIOS : a BioInformatics Oriented Service architecture for RNA-seq analysis. 20

CycADS annotation database system to support the development and update of enriched BioCyc databases 22

FrameDP: sensitive peptide detection on noisy matured sequences 23

iANT : integrated ANnotation Tool 24

Portail Meloidogyne incognita 26

Legoo : a bioinformatics gateway towards integrative legume biology 28

REMORA : un poisson pilote dans l'océan des web-services BioMOBY 30

Axe 2 : Génomique comparative et caractérisation de la biodiversité 32

CFBP : Collection Française de Bactéries associées aux Plantes 33

E-phytia et Di@gnoPlant® : un continuum de services du Web au terrain en protection des plantes 34

Florapis : base de données photographiques et bibliographiques sur le butinage des abeilles domestiques 36

La base R-SYST : identification des espèces de groupes d'organismes d'intérêt 38

Narcisse : navigateur de génomes comparés 40

SESAME (SEquence Sorter & AMplicon Explorer): genotyping based on high-throughput multiplex amplicon sequencing 42

Abstract 42

Axe 3: Intégration et Représentation des Connaissances 43

MetExplore: Collaborative platform for building, analyzing, simulating and improving metabolic networks 44

Exemple de Projet Structurant du futur CATI 46

BBRIC WORKSPACE 47

Projets Phares

Axe 1: Organisation et régulation des génomes

ANAIS: Analysis of NimbleGen Arrays Interface

http://anais.versailles.inra.fr

Adeline Simon¹, Eric Biot²

¹UR1290 BIOGER−CPP, INRA, Grignon

²Institut Jean-Pierre Bourgin, UMR1318, INRA-AgroParisTech, Versailles, France

Contact: [e-mail]

Publication : Simon A, Biot E. (2010). ANAIS: Analysis of NimbleGen Arrays Interface. Bioinformatics 2010 Oct; 26(19):2468-9.
Summary: ANAIS is a user-friendly web-based tool for the processing of NimbleGen expression data. The interface reads single-channel microarray files generated by NimbleGen platforms and produces easily interpretable graphical and numerical results. It provides biologists six turnkey analysis modules—normalization, probe to gene, quality controls, differential expression, detection, queries and clustering—to explore quickly, freely and without the need for computer programming, NimbleGen transcriptome data.
May 2012 inventory :

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  206 users since july 2010
  
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  442 projects currently on the server
  
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  3 citing articles :
  

Title : Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations.

Author(s): Rouxel T. et al.

Source : Nat Commun. 2011 Feb;2:202.

Title : Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Author(s): Amselem A. et al.

Source: PLoS Genetics. 2011 Aug;7(8):e1002230
Title : HdfR is a regulator in Photorhabdus luminescens that modulates metabolism and symbiosis with the nematode Heterorhabditis

Author(s) : Easom CA. and Clarke DJ.

Source : Environmental Microbiology (2012) 14: 953

ANATool : The Arabidopsis Natural Accession Tool

https://www.versailles.inra.fr/ijpb/crb/anatool

Matthieu Simon¹, Adeline Simon², Fréderic Martins³, Lucy Botran¹, Sébastien Tisné¹, Fabienne Granier¹, Olivier Loudet¹ and Christine Camilleri¹

¹Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78000 Versailles, France

²BIOGER, UR1290 INRA-AgroParisTech, 78850 Thiverval-Grignon, France

³Plateforme Génomique, Génopole Toulouse/Midi-Pyrénées, 31326 Castanet-Tolosan, France

Contact for biology: [e-mail]

Contact for bioinformatics: [e-mail]

Publication : Simon M, Simon A, Martins F, Botran L, Tisné S, Granier F, Loudet O, Camilleri C (2012). DNA fingerprinting and new tools for fine-scale discrimination of Arabidopsis thaliana accessions. Plant J. 2012 Mar;69(6):1094-101.
Summary: The Arabidopsis Natural Accession Tool web interface was developed for the Arabidopsis community to provide access to all fingerprinting data obtained on natural accessions managed at the Arabidopsis thaliana Resource Centre for Genomics at INRA Versailles, France.

The genotyping assay was performed at the Genomics facility at INRA Toulouse, France using a GoldenGate assay which interrogates all 384 SNPs simultaneously and VeraCode technology was used for reading. The final data matrix of 341 informative markers for 591 accessions is available through the ANATool interface

The smallest number of markers that uniquely defines each haplotype was defined. This pattern is called a fingerprint and is composed of a combination of different SNPs for each haplotype.

From the ANATool interface, four types of queries can be submitted to (1) find the fingerprint of a given accession; (2) find genotypes from a selection of accessions and markers; (3) find accessions from a selection of markers and genotypes; and (4) find the minimal marker set required to distinguish among a set of given accessions. Optimized SNP sets are also available to quickly fingerprint natural accessions of Arabidopsis. Thus, ANATool is a simple, readily accessible and fast (only DNA fragments need to be sequenced) tool for confirming the identity of accessions at any laboratory working on Arabidopsis.

The development of ANATool was funded by INRA and by the French national biomedical, biological and agricultural research infrastructures network GIS-IBiSA.