Methods for automated genome-scale metabolic model reconstruction. (20th August 2018)

• Record Type: Journal Article
• Authors: Faria, José P.; Rocha, Miguel; Rocha, Isabel; Henry, Christopher S.
• Is Part Of: Biochemical Society transactions. Volume 46:Number 4(2018)
• Page Start: 931
• Page End: 936
• Publication Date: 2018-08-20
• Subjects: genome annotation -- genome-scale metabolic model -- metabolic network; Biochemistry -- Congresses; 572
• DOI: 10.1042/BST20170246
• Languages: English
• ISSNs: 0300-5127

Abstract

Abstract : In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. Here, we are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin .