Generation Challenge Programme

Genomics research software

The software on this page, to which its development the GCP contributed, is applicable in the field of genomics research.
Below you will find links with brief information for these products.

   Dayhoff - a comparative stress gene catalog

The GCP has developed Dayhoff, the ortholog gene catalogue. (http://202.123.56.214:8080/DayhoffWeb2/) Dayhoff documents stress-responsive genes comparatively across plant species. It is a compendium of protein families, phylogenetic trees and multiple sequence alignments with the associated experimental evidence. It serves to elucidate orthologous and paralogous relationships between plant genes that may be involved in response to environmental stress, mainly abiotic stresses such as water deficit (‘drought’). For example, the comparison of microarray data about drought stress obtained across diverse crop species can be analysed in a comparative manner to identify common gene expression profiles under similar stresses. The web site includes query and visualization tools and allows searches and browsing of the underlying project database. (read more)

GreenPhylDB - a phylogenomic database for plant comparative genomics

GreenPhylDB is a phylogenomic database for plant comparative genomics. GreenPhylDB offers the most complete plant family list and is manually curated. The major part of these families have been analyzed with the CIRAD optimized phylogenomic pipeline. In addition, GreenPhylDB includes GOST (GreenPhyl Orthologs Search Tool) to predict phylogenomic relationships between any plant sequence gene and O.sativa /A.thaliana gene(s) (read more).

GOST - GreenPhyl orthologs search tool

GOST (GreenPhyl Orthologs Search Tool) is a web site developed by GCP to predict phylogenomic relationships between any plant gene and Oryza sativa and / or Arabidopsis thaliana gene(s). GOST rapidly infers ortholog relationships by integrating a new sequence into a model phylogeny developed on these plant species. GOST is based on GreenphylDB, a phylogenomic database for plant comparative genomics and the most complete plant family list manually curated. GreenPhylDB is the comprehensive platform for comparative genomic analyses of Arabidopsis thaliana and Oryza sativa full genomes.

DARwin - Dissimilarity Analysis and Representation for Windows

DARwin (Dissimilarity Analysis and Representation for Windows) is a popular, well designed software package developed by GCP. It offers diversity and phylogenetic analysis. Nucleic sequences, amino acid sequences, molecular markers, and qualitative or quantitative characters can be utilised to infer and transform dissimilarity matrices. Different algorithms are available for factorial analyses, tree construction and the accession of their reliability. Several trees based on the same data set can be compared. Ease readible graphics can be made.

CMTV - Comparative Map and Trait Viewer

The Comparative Map and Trait Viewer (CMTV) is tool for constructing consensus maps and comparing QTL and functional genomics data across genomes and experiments. The CMTV is a graphical user interface developed for constructing complex visualizations of genetic and genomic data collected from a variety of sources. It was designed to provide researchers with an intuitive mechanism to compare and integrate their own local mapping data with data from public databases, as well as to enable the aggregation of data from disparate sources into a common representational framework. GCP supported the development of this program into an open source Java code. (brochure) (read more)

RiCES - Rice Cis-Element Searcher

RiCES is a cis-element searching tool optimized for rice (Oryza sativa) genome. It takes as input a list of identifiers of transcription unit IDs of Oryza sativa, defined in Pseudomolecule corresponding to KOME full length cDNA clones, and returns a list of cis-element sites that appear to be shared across the listed gene loci. The motif searching program, MEME, is applied in the front step of the analysis. The RiCES tool is available as webservice. (read more)

RiceGeneThresher 2.0 - interface to find the stress-responsive genes and their location

RiceGeneThresher is a web-based application for mining genes underlying QTLs in the Rice genome. RiceGeneThresher incorporated the “The Generation Challenge Programme Comparative Plant Stress-responsive Gene Catalogue” on http://dayhoff.generationcp.org/ for an online resource documenting stress-responsive genes comparatively across plant species (Wanchana, Thongjuea et al. 2008). RiceGeneThresher provides user friendly interface to find the stress-responsive genes and their location in the genome region of interest.

OryGenesDB - an interactive tool for rice reverse genetics

The OryGenesDB CIRAD-based webservice originated from the the Oryza sativa database.
Sequence information is linked with related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data, etc). Data sources are available for rice (spp. indica and spp. japonica, sorghum and Arabidopsis. A genome Browser (Gbrowse), displaying genomic annotations and other features, is the core of this database. The reference annotation layer consists in the 12 rice pseudomolecules released by the TIGR (Version 5.0, January 2007). All the data are superposed as annotations layers and positioned with respect to these pseudomolecules. A set of tools around GBrowse was developed to retrieve as exhaustively as possible information related to queries with several starting points.
In addition, Orylink can be found on this website, offering a personal and integarted system for functional genomic analysis.

GenDiversity - combining decentralised genotyping data for diversity analysis

GenDiversity, a webservice developed at CIRAD, is a query and analysis application which combines genotyping data from several data sources, developed in support of diversity studies.
GenDiversity offers different functionalities: querying genotyping data from different databases (the GCP Central Registry, Tropgene, IRIS), combining two or more different genotyping studies, filtering by passport data, computation of allelic frequencies, computation of LD, and checking for duplicates. Gendiversity can convert the outputs to the file format of choice, suitable for diversity analysis (DARwin, Convert, Structure, Haploview).

Core Hunter - the genetic resource sampling software

Core Hunter is a highly effective and flexible tool for sampling genetic resources from a reference data set and for establishing core subsets. Core Hunter uses an advanced stochastic local search algorithm for selecting core subsets. Users can specify the sampling intensity and which genetic measures will be used for selection criteria.
Core Hunter is provided with an algorithm capable of selecting core subsets with a high average genetic distance between accessions, or rich genetic diversity overall, or a combination of both. As such it accommodates the formation of diverse types of subsets, either based on breeder’s preferenceres for allele representativeness, or taxonomist’s preferences for allele richness.

The contribution of the Generation Challenge Programme to the development of the above software packages varied from support for translation to complete funding.

More analytic software is available via the High Performance Computing grid.