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Genome

Genomic data can be visualized through different tools :

  • Genomic browsers to  display annotations available mapped on genome. Gene editing could be available through XebApollo in the frame of collaborative projects
  • Synteny browsers between 2 or more genomes
  • Gene report tool  combining structural and functional annotation gene centered

See details below to get a a brief description

Genomic browsers:

 GnpGenome is the genomic module of the INRA URGI information system (GnpIS). It is used to store whole genomes or large genomic fragments sequences (BAC, chromosomes...) and their annotations data (all data that can be mapped on genomes: genes, repeats, genetic markers (SSR, microsatellites...), SNPs markers, oligos, probes/array, QTL, metaQTLs...).

GnpGenome can also be used to store physical maps, for example for Wheat, for Maize. To submit physical maps, you can provide FPC software results. Have a look on Data/Submission page, for more information about data submission process and contact us if you need more information.

We can link also the two types of databases: GnpGenome sequence annotations with GnpGenome physical data, for example on Wheat genome.

Several instances of GBrowse or JBrowse are available according to species and depending also the version of assembly : for example, we have one database for wheat, 2 for grape (8X and 12X), Botrytis, Leptosphaeria, poplar (V1, V2), Arabidopsis. apple, tomato.).

Technically, this module is composed of database (Chado schema, BioSeqDbFeature schema and MySQL) and interfaces (GBrowse, JBrowse, WebApollo) based on the Generic Model Organism Database (GMOD) Project (open source project), that is used in particular for our gene annotation and curation workflow. We also use .

The data insertion format is built over the standart GFF3 format , which is a simple tab-delimited format used to represent genomic features and permits a hierarchical way of representating them. 

Synteny browsers :

Two different tools are available to browse synteny data:

  • the Plant Synteny viewer, a new tool that we developped at URGI, to display genes syntenies on chromosomes, between ancestral genomes.

WHEAT SYNTENOME UNVEILS NEW EVIDENCES OF CONTRASTED EVOLUTIONARY PLASTICITY BETWEEN PALEO- AND NEODUPLICATED SUBGENOMES

Pont, Caroline; Murat, Florent; Guizard, Sebastien; Flores, Raphael; Foucrier, Severine; Bidet, Yannick; Quraishi, Umar Massod; Alaux, Michael; Dolezel, Jaroslav; Fahima, Tzion; Budak, Hikmet; Keller, Beat; Salvi, Silvio; Maccaferri, Marco; Steinbach, Delphine; Feuillet, Catherine; Quesneville, Hadi; Salse, Jerome

The Plant Journal, in press

Launch Wheat synteny viewer

  • Gbrowse_syn viewer, a GMOD tool that we used to display syntenies between 2 or more related genomes.

Gene editing, gene curation:

  • We use WebApollo for manual gene curation and editing. This tool is a GMOD tool allowing gene editing and curation in the frame of large collaborative projects involving annotations groupes (experts) of gene families. 

 Gene reports :

  • The GRS tool was developped to build gene centered reporting, compiling data from gene structural and functional annotations. See more details on ANR GnpAnnot project page and GRS tool. For example, we are currently using it for our fungal genome.   

See also Genome Data submission page for details concerning data submission process

See also Genome access page to get the list of all genomes that we have on the web site and to query them

Do not hesitate to contact us at urgi-support if you need more support on data submission . We could also give you advices on GFF3 format so that it could be compatible both for Gbrowse/JBrowse visualization.


Update: 22 Jan 2016
Creation date: 28 Apr 2010