SNP

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)

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

TropGeneDB

TropGeneDB is a component of the South Green Bioinformatics Platform for the management of genetic, molecular and phenotypic data on tropical crop species. The most common data stored in TropGeneDB are molecular markers, QTLs (Quantitative Trait Loci), genetic and physical maps, genetic diversity, phenotypic diversity studies, and information on genetic resources (geographic origin, parentage, collection). TropGeneDB is organized on a crop basis with currently nine public modules (banana, cocoa, coconut, coffee, cotton, oil palm, rice, rubber tree, sugarcane).

gene database for tropical plants
Referent(s): 
Chantal Hamelin, Manuel Ruiz
Funding: 

This project is mainly supported by CIRAD core funding.

SNiPlayDB

SNiPlay is a web-based tool for SNP and polymorphism analysis. From sequencing traces, alignment or allelic data given as input, it detects or extracts SNP and insertion/deletion events. In a second step, it sends sequences and allelic data into an integrative pipeline

SNP and polymorphism analysis
Referent(s): 
Alexis Dereeper
Funding: 

ANR DLVitis (2009), ANR GnpAsso (2012)

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