Cocoa pods, Venezuela. Photo: C.Lanaud ©CIRAD
Arabica coffee, Ethiopia. Photo: ©Jean-Pierre Labouisse
Yams in Benin. Photo: J-L Pham ©IRD
Rice harvest, Guinea. Photo: J-L Pham ©IRD
Maize corn. Photo: ©Brigitte Gouesnard

Actions carried out

WP1. Development of a collaborative bioinformatics network

Task 1.1 - Cataloguing existing software and resources belonging to participating institutions; integrating them and making them accessible via a single exploitation system.
Task 1.2 - Promoting the full integration of tools such as the interoperability of databases, homogenization of workflows with common modules, development of generic graphic and query interfaces on the Web.
Task 1.3 - Creation of a Web portal to access all regional bioinformatics resources.
Task 1.4 - Participation in meetings organized by the different ARCAD sub-projects.
Task 1.5 - Organization of training in bioinformatics.
Task 1.6 - Diffusion of information about the ARCAD project: Web portal, publications, international conferences.
Task 1.7 - Starting and/or maintaining collaborative projects with other national and international bioinformatics platforms (Bioinfo-GenoToul, URGI, CNG, GCP, GMOD).
Task 1.8 – Promoting a quality management system in compliance with the IBISA label and the ISO 9001 standard.

WP2. Module for data management

Task 2.1 - Data management: data collection, data storage and formatting.
Task 2.2 - Adaptation of existing databases: components of existing databases will be reused, Chado (genomics annotation), TropGene (markers, maps, phenotypes, QTL), GreenPhyl (phylogenomic information) and development of new components.
Task 2.3 - Controlled integration in database modules.
Task 2.4 - Integration of external data: i) Links between environments, phenotypes, genetic resources, and genotyping data (SNP), ii) Links between genotyping data (SNP), QTL, association values, and sequence genomics annotations
Task 2.5 - Development of Web interfaces based on user needs.
Task 2.6 - Regular interactions with the data providers: helpdesk, soliciting feedback, training, presentations of the ARCAD database.

WP3. Module for diversity analyses

Task 3.1 - Assembling 454 sequencing outputs, testing of methods and parameters.
Task 3.2 - SNP determination.Task 3.3 - Link to genotyping data (Illumina chips).
Task 3.4 - Haplotypes definition.Task 3.5 - Detection of intra-species selection.
Task 3.6 - Development of integrated convivial Web interfaces.
Task 3.7 - Regular interactions with the ARCAD scientific projects concerning diversity analyses.

WP4. Module for sequence annotation and orthologue gene prediction

Task 4.1 - Automatic sequence annotation using manually curated sources (e.g. UniProtKB/Swiss-Prot), protein domains and others.
Task 4.2 - Improvement of existing tools (GOST) to allow high-throughput sequence analysis.
Task 4.3 - Prediction of paralogue and orthologue genes using phylogenetic methods.
Task 4.4 - Further development of Web interfaces for the visualization of analyses.
Task 4.5 - Detection of the inter-species selection.
Task 4.6 - Characterization of the evolutionary dynamics of orthologues (genetic divergence, codon usage, GC content, etc.), and availability of the descriptors through a database like OrthoMaM (Ranwez et al. 2007).
Task 4.7 - Interactions with ARCAD research teams concerned with comparative genomics (evolution and domestication, functional analyses).

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