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

doi:10.1093/bioinformatics/btab622

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

Bioinformatics. 2021 Nov 5;37(21):3974-3975. doi: 10.1093/bioinformatics/btab622.

Authors

Almut Heinken^{1

2}, Stefanía Magnúsdóttir³, Ronan M T Fleming^{1

4}, Ines Thiele^{1

2

5

6}

Affiliations

¹ School of Medicine, National University of Galway, H91 TK33 Galway, Ireland.
² Ryan Institute, National University of Galway, H91 TK33 Galway, Ireland.
³ Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands.
⁴ Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands.
⁵ Division of Microbiology, National University of Galway, H91 TK33 Galway, Ireland.
⁶ APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland.

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Genome
Genomics
Metabolic Networks and Pathways*
Molecular Sequence Annotation
Software*

Abstract

Publication types

MeSH terms

Grants and funding