Integrative system for gene family gathering and analysis in a context of crops stress response study : [P1050]
The study of plant tolerance to stress is a crucial issue for crops improvement and stability in constrained environments. Gene family analysis is an important way to understand complex processes underlying stress response in crops. Several tools exist to study families and propose automatically clustered families or curated published families. We observed that automatic clustering, efficient for global analyses, is rarely sufficient for precise studies: i) families can be spread in several cluster, or ii) intrusive sequences are represented in clusters of interest. That is why biologists need most of the time to manually constitute their families. In response to this need, we propose to develop an integrative system that will allow to gather sequences from different sources for a customized family. This system will integrate several tools used for family construction and analysis. Currently, the prototype allows to query in-house Chado database (banana, coffee) and to import personal data with a web interface using the Drupal CMS. Multi-species analyzes are available using Galaxy workflows manager. Eventually, this system will be linked to a stress response oriented database. This database will propose a set of controlled vocabularies, some known stress resistance factors and other indicators to ease the identification of mechanisms implied in plant stress resistance. Beside that, this system will be generic for all type of gene families, and will propose a synthetic and dynamic view to offer to researchers an easy and intuitive way to curate their families. (Texte intégral)
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Subjects: | F30 - Génétique et amélioration des plantes, F60 - Physiologie et biochimie végétale, H50 - Troubles divers des plantes, |
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dig-cirad-fr-5732752019-12-01T17:02:07Z http://agritrop.cirad.fr/573275/ http://agritrop.cirad.fr/573275/ Integrative system for gene family gathering and analysis in a context of crops stress response study : [P1050]. Larivière Delphine, Dufayard Jean-François, Bocs Stéphanie, This Dominique. 2014. In : Plant and Animal Genomes Conference XXII Conference, San diego, United States, San Diego, United States, January 11-15, 2014. s.l. : s.n., Résumé Plant and Animal Genome Conference. 22, San Diego, États-Unis, 11 Janvier 2014/15 Janvier 2014.https://pag.confex.com/pag/xxii/webprogram/Paper9428.html <https://pag.confex.com/pag/xxii/webprogram/Paper9428.html> Researchers Integrative system for gene family gathering and analysis in a context of crops stress response study : [P1050] Larivière, Delphine Dufayard, Jean-François Bocs, Stéphanie This, Dominique eng 2014 s.n. Plant and Animal Genomes Conference XXII Conference, San diego, United States, San Diego, United States, January 11-15, 2014 F30 - Génétique et amélioration des plantes F60 - Physiologie et biochimie végétale H50 - Troubles divers des plantes The study of plant tolerance to stress is a crucial issue for crops improvement and stability in constrained environments. Gene family analysis is an important way to understand complex processes underlying stress response in crops. Several tools exist to study families and propose automatically clustered families or curated published families. We observed that automatic clustering, efficient for global analyses, is rarely sufficient for precise studies: i) families can be spread in several cluster, or ii) intrusive sequences are represented in clusters of interest. That is why biologists need most of the time to manually constitute their families. In response to this need, we propose to develop an integrative system that will allow to gather sequences from different sources for a customized family. This system will integrate several tools used for family construction and analysis. Currently, the prototype allows to query in-house Chado database (banana, coffee) and to import personal data with a web interface using the Drupal CMS. Multi-species analyzes are available using Galaxy workflows manager. Eventually, this system will be linked to a stress response oriented database. This database will propose a set of controlled vocabularies, some known stress resistance factors and other indicators to ease the identification of mechanisms implied in plant stress resistance. Beside that, this system will be generic for all type of gene families, and will propose a synthetic and dynamic view to offer to researchers an easy and intuitive way to curate their families. (Texte intégral) conference_item info:eu-repo/semantics/conferenceObject Conference info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/573275/1/document_573275.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://pag.confex.com/pag/xxii/webprogram/Paper9428.html info:eu-repo/semantics/altIdentifier/purl/https://pag.confex.com/pag/xxii/webprogram/Paper9428.html |
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F30 - Génétique et amélioration des plantes F60 - Physiologie et biochimie végétale H50 - Troubles divers des plantes F30 - Génétique et amélioration des plantes F60 - Physiologie et biochimie végétale H50 - Troubles divers des plantes |
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F30 - Génétique et amélioration des plantes F60 - Physiologie et biochimie végétale H50 - Troubles divers des plantes F30 - Génétique et amélioration des plantes F60 - Physiologie et biochimie végétale H50 - Troubles divers des plantes Larivière, Delphine Dufayard, Jean-François Bocs, Stéphanie This, Dominique Integrative system for gene family gathering and analysis in a context of crops stress response study : [P1050] |
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The study of plant tolerance to stress is a crucial issue for crops improvement and stability in constrained environments. Gene family analysis is an important way to understand complex processes underlying stress response in crops. Several tools exist to study families and propose automatically clustered families or curated published families. We observed that automatic clustering, efficient for global analyses, is rarely sufficient for precise studies: i) families can be spread in several cluster, or ii) intrusive sequences are represented in clusters of interest. That is why biologists need most of the time to manually constitute their families. In response to this need, we propose to develop an integrative system that will allow to gather sequences from different sources for a customized family. This system will integrate several tools used for family construction and analysis. Currently, the prototype allows to query in-house Chado database (banana, coffee) and to import personal data with a web interface using the Drupal CMS. Multi-species analyzes are available using Galaxy workflows manager. Eventually, this system will be linked to a stress response oriented database. This database will propose a set of controlled vocabularies, some known stress resistance factors and other indicators to ease the identification of mechanisms implied in plant stress resistance. Beside that, this system will be generic for all type of gene families, and will propose a synthetic and dynamic view to offer to researchers an easy and intuitive way to curate their families. (Texte intégral) |
format |
conference_item |
topic_facet |
F30 - Génétique et amélioration des plantes F60 - Physiologie et biochimie végétale H50 - Troubles divers des plantes |
author |
Larivière, Delphine Dufayard, Jean-François Bocs, Stéphanie This, Dominique |
author_facet |
Larivière, Delphine Dufayard, Jean-François Bocs, Stéphanie This, Dominique |
author_sort |
Larivière, Delphine |
title |
Integrative system for gene family gathering and analysis in a context of crops stress response study : [P1050] |
title_short |
Integrative system for gene family gathering and analysis in a context of crops stress response study : [P1050] |
title_full |
Integrative system for gene family gathering and analysis in a context of crops stress response study : [P1050] |
title_fullStr |
Integrative system for gene family gathering and analysis in a context of crops stress response study : [P1050] |
title_full_unstemmed |
Integrative system for gene family gathering and analysis in a context of crops stress response study : [P1050] |
title_sort |
integrative system for gene family gathering and analysis in a context of crops stress response study : [p1050] |
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url |
http://agritrop.cirad.fr/573275/ http://agritrop.cirad.fr/573275/1/document_573275.pdf |
work_keys_str_mv |
AT larivieredelphine integrativesystemforgenefamilygatheringandanalysisinacontextofcropsstressresponsestudyp1050 AT dufayardjeanfrancois integrativesystemforgenefamilygatheringandanalysisinacontextofcropsstressresponsestudyp1050 AT bocsstephanie integrativesystemforgenefamilygatheringandanalysisinacontextofcropsstressresponsestudyp1050 AT thisdominique integrativesystemforgenefamilygatheringandanalysisinacontextofcropsstressresponsestudyp1050 |
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1758024161684357120 |