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

2021/06/11 by Heinken, Almut, Magnúsdóttir, Stefanía, Fleming, Ronan M. T. +1 · 1 citation
#FOS: Biological sciences #Genomics (q-bio.GN) #Molecular Networks (q-bio.MN)

paper · doi:10.48550/arxiv.2106.06638

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.

Cited by

• Dietary patterns influence the in silico GABA production capacity of Bifidobacterium adolescentis HD17T2H and other human gut bacteria

Related

• MoGAAAP: A modular Snakemake workflow for automated genome assembly and annotation with quality assessment
• OmniGenBench: Automating Large-scale in-silico Benchmarking for Genomic Foundation Models
• orthogene: a Bioconductor package to easily map genes within and across hundreds of species
• DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome
• GBRAP: A Comprehensive Database and Tool for Exploring Genomic Diversity Across All Domains of Life