SNP

Grass Genome Hub

An Information System for comparative and functional genomics dedicated to Grasses species

Rice Genome Hub

The Rice Genome Hub is an integrative genome information system that allows centralized access to genomics and genetics data, and analytical tools to facilitate translational and applied research in rice. The hub is built using the Content Management System Drupal with the Tripal module that interacts with the Chado database. The Hub interface provides several functionalities (Blast, DotPlots, Gene Search, JBrowse, Primer Blaster, Primer Designer) to make it easy for querying, visualizing and downloading research data.

an integrative genome information system that allows centralized access to genomics and genetics data
Referent(s): 
Manuel Ruiz, Gaëtan Droc

Gigwa

 

Easily manage, share, explore, visualize NGS genotyping data.
Support for VCF, Hapmap, PLINK formats, RESTful standards, Galaxy and FlapJack connectivity.

 

Gigwa helps managing, sharing, and exploring high density genotyping data (typically VCF files)
Funding: 

This project was funded by Agropolis Fondation under the reference ID ARCAD 0900-001.

AgroLD

 

The Agronomic Linked Data knowledge graph database for plant molecular data
Referent(s): 
Pierre Larmande
Funding: 

IBC - Institut de Biologie Computationnelle

IFB - Institut Francais de Bioinformatique

Cassava Genome Hub

the integrated portal for cassava
Referent(s): 
Manuel Ruiz, Alexis Dereeper
Funding: 

Agropolis Fondation (Twin post-doc)

Coffee Genome Hub

The Coffee Genome Hub is an integrated web-based database providing centralized access to coffee community genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee.

the integrated portal for coffee
Funding: 

The research was funded by the French National Research Agency, Australian Research Council, Natural Sciences and Engineering Research Council of Canada, CNR-ENEA Agrifood Project of Italy, Funding Authority for Studies and Projects (FINEP) of Brazil, National Institutes of Science and Technology (INCT) of Brazil, the U.S. National Science Foundation and the College of Arts and Science, University at Buffalo.

Cocoa Genome Hub

Access the cocoa Criollo Genome Version 2 with 99% of the genes anchored to the 10 chromosomes

a Web portal for crossing cocoa phenotypic, genetic and genomic data from ICGD and TropGeneDB databases
Referent(s): 
Gaëtan Droc

Banana Genome Hub

The Banana Genome Hub centralises databases of genetic and genomic data for the musa acuminata crop Hub developed by Cirad and Bioversity and supported by the South Green Bioinformatics platform. Data available are the complete genome sequence along with gene structure, gene product information, metabolism, gene families, transcriptomics (ESTs, RNA-Seq), genetic markers (SSR, DArT, SNPs) and genetic maps.

the integrated crop portal for Musa
Funding: 

ANR

OryGenesDB

 

OryGenesDB is a database developed for rice reverse genetics. OryGenesDB contains FSTs (flanking sequence tags) of various mutagens and functional genomics data collected from both international insertion collections and the literature.

Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database.

Oryza Genes Database
Referent(s): 
Gaëtan Droc
Funding: 

Genoplante, EU (Cereal Gene Tags)

GNPAnnotDB

 

GNPAnnot is a Community Annotation System (CAS) for structural, functional and comparative annotation dedicated to green genomes see details of the project in the project section.

a generic Community Annotation System
Referent(s): 
Stéphanie Bocs
Funding: 

ANR Genoplante

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