Gene

GIGWA

Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions.

Gigwa aims at managing and searching genotyping data from NGS analyses
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).

 

Oryza Tag Line

Oryza Tag Line consists in a searchable database integrating phenotypic data resulting from the evaluation of the Génoplante rice insertion line library.

Oryza Tag Line database
Referent(s): 
Pierre Larmande
Funding: 

Génoplante

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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