GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics
2022
Summo, Marilyne | Comte, Aurore | Martin, Guillaume | Perelle, Pierrick | Weitz, Eric, M | Droc, Gaëtan | Rouard, Mathieu | Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM) | Département Systèmes Biologiques (Cirad-BIOS) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad) | South Green Bioinformatics Platform [Montpellier] | Plant Health Institute of Montpellier (UMR PHIM) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM) | Broad Institute of MIT and Harvard (BROAD INSTITUTE) ; Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston] | The Alliance of Bioversity International and International Center for Tropical Agriculture (CIAT) [France] ; Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome] (Alliance) ; Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR) | GeMo has been developed in the framework of the Agropolis Fondation (ID 1504–006) ‘GenomeHarvest’ project through the French Investissements d’avenir programme (Labex Agro: ANR-10-LABX-0001). This work was supported by the CIRAD—UMR AGAP HPC Data Center of the South Green Bioinformatics platform (http://www.southgreen.fr). | ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Data processing instructions, scripts and documentation are available at https://gemo.readthedocs.io. GeMo is primarily designed for online access on our servers, but code source is open access on GitHub at https://github.com/SouthGreenPlatform/GeMo and can be used for local set up.
Mostrar más [+] Menos [-]International audience
Mostrar más [+] Menos [-]Inglés. Abstract: In silico chromosome painting is a technique by which contributions of distinct genetic groups are represented along chromosomes of hybrid individuals. This type of analysis is used to study the mechanisms by which these individuals were formed. Such techniques are well adapted to identify genetic groups contributing to these individuals as well as hybridization events. It can also be used to follow chromosomal recombinations that occurred naturally or were generated by selective breeding. Here, we present GeMo, a novel interactive web-based and user-oriented interface to visualize in a linear-based fashion results of in silico chromosome painting. To facilitate data input generation, a script to execute analytical commands is provided and an interactive data curation mode is supported to ensure consistency of the automated procedure. GeMo contains preloaded datasets from published studies on crop domestication but can be applied to other purposes, such as breeding programs Although only applied so far on plants, GeMo can handle data from animals as well. Database URL: https://gemo.southgreen.fr/
Mostrar más [+] Menos [-]Información bibliográfica
Este registro bibliográfico ha sido proporcionado por Institut national de la recherche agronomique