DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations
Almut Heinken, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele
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Abstract
Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account. Results: We developed DEMETER, a COBRA Toolbox extension that 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: DEMETER and tutorials are available at https://github.com/opencobra/cobratoolbox.