UP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction.

ABSTRACT: Overexpression of key genes is a basic strategy for overproducing target products via metabolic engineering. Traditionally, identifying those key genes/pathways largely relies on the knowledge of biochemistry and bioinformatics. In this study, a modeling tool named UP Finder was developed to facilitate the rapid identification of gene overexpression strategies. It was based on the COBRA toolbox under MATLAB environment. All the key gene/pathway targets are identified in one click after simply loading a Systems Biology Markup Language model and specifying a metabolite as the targeted product. The outputs are also quantitatively ranked to show the preference for determining overexpression strategies in pathway design. Analysis examples for overproducing lycopene precursor in Escherichia coli

SUBMITTER: Wang X 

PROVIDER: S-EPMC5699525 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature