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

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

Sup

SUBMITTER: Heinken A 

PROVIDER: S-EPMC8570805 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature