DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations.

Autor:	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.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2021 Nov 05; Vol. 37 (21), pp. 3974-3975.
DOI:	10.1093/bioinformatics/btab622
Abstrakt:	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.)
Databáze:	MEDLINE
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