High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
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Le résumé fourni par la source
The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed.
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Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
- Date Crossref
- 09/06/2014
- Éditeur
- National Academy of Sciences
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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University of Chicago Computation Institute pays non établi dans la noticeUniversité ou école supérieure
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University of Horticultural Sciences Bagalkote pays non établi dans la noticeUniversité ou école supérieure
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University of Florida Department of Microbiology and Cell Science pays non établi dans la noticeUniversité ou école supérieure
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Cold Spring Harbor Laboratory pays non établi dans la noticeOrganisation à but non lucratif
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Argonne National Laboratory and Life Sciences pays non établi dans la noticeStructure de recherche
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Agricultural Research Service pays non établi dans la noticeOrganisme public
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Cornell University Soil and Nutrition Laboratory Research Unit pays non établi dans la noticeUniversité ou école supérieure
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Mathematics and Computer Science Division and pays non établi dans la noticeInstitution
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Fellowship for Interpretation of Genomes pays non établi dans la noticeInstitution
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Horticultural Sciences Department and pays non établi dans la noticeInstitution
Computation Institute — University of Chicago, University of Horticultural Sciences Bagalkote et Department of Microbiology and Cell Science — University of Florida, avec 7 autres affiliations.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.