학술논문
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations.
Document Type
Academic Journal
Author
Heinken A; School of Medicine, National University of Galway, H91 TK33 Galway, Ireland.; Ryan Institute, National University of Galway, H91 TK33 Galway, Ireland.; Magnúsdóttir S; Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands.; Fleming RMT; School of Medicine, National University of Galway, H91 TK33 Galway, Ireland.; Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands.; Thiele I; School of Medicine, National University of Galway, H91 TK33 Galway, Ireland.; Ryan Institute, National University of Galway, H91 TK33 Galway, Ireland.; Division of Microbiology, National University of Galway, H91 TK33 Galway, Ireland.; APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland.
Source
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Subject
Language
English
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.
(© The Author(s) 2021. Published by Oxford University Press.)
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.
(© The Author(s) 2021. Published by Oxford University Press.)