Gene

Sugarcane Genome Hub

The Sugarcane Genome Hub is an integrated web-based database providing centralized access to the sugarcane reference genome sequences and genomic resources. Data currently available is the monoploid reference genome sequence obtained from R570 cultivar. This web portal is built using open-source Tripal database infrastructure. It is developed by CIRAD and supported by the South Green Bioinformatics platform.

The Sugarcane Genome Hub is an integrated web-based database providing centralized access to the sugarcane reference genome sequences and genomic resources.
Referent(s): 
Gaëtan Droc

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)

EURoot

EURoot DB is the database of the EURoot project "Enhancing resource uptake from roots under stress in cereal crops

the database on QTLs, genes and mutants involved in root growth under stress of the EURoot project "Enhancing resource uptake from roots under stress in cereal crops"
Referent(s): 
Chantal Hamelin
Funding: 

EU

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.

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

GreenPhylDB

GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. Version 3 now contains 22 full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families.

a curated catalogue of plant gene families for a quest for orthologs
Funding: 

This project was supported by the Generation Challenge Program (GCP) and the Agropolis foundation (ARCAD) and is currently supported by Syngenta and the CGIAR Research Program (CRP) on Roots, Tubers, and Bananas (RTB).

 

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