Dataset Information
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations.
Ontology highlight
ABSTRACT: Motivation
Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools do not typically take species-specific experimental and curated genomic data into account.Results
We developed Data-drivEn METabolic nEtwork Refinement (DEMETER), a Constraint-Based Reconstruction and Analysis (COBRA) Toolbox extension, which enables the efficient, simultaneous refinement of thousands of draft genome-scale reconstructions, while ensuring adherence to the quality standards in the field, agreement with available experimental data and refinement of pathways based on manually refined genome annotations.Availability and implementation
DEMETER and tutorials are freely available at https://github.com/opencobra.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Heinken A
PROVIDER: S-EPMC8570805 | biostudies-literature | 2021 Nov
REPOSITORIES: biostudies-literature
Publications
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations.
Bioinformatics (Oxford, England) 20211101 21
<h4>Motivation</h4>Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools do not typically take species-specific experimental and curated genomic data into account.<h4>Results</h4>We developed Data-drivEn METabolic nEtwork Refinement (DEMETER), a Constraint-Based Reconstruction and Analysis (COBRA) Toolbox extension, which enables the efficient, simultaneous refinement of thousands of draft genome-scale reconstructions, while ensuring adherence to the ...[more]