GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction.

ABSTRACT: Metabolic network models are increasingly being used in health care and industry. As a consequence, many tools have been released to automate their reconstruction process de novo. In order to enable gene deletion simulations and integration of gene expression data, these networks must include gene-protein-reaction (GPR) rules, which describe with a Boolean logic relationships between the gene products (e.g., enzyme isoforms or subunits) associated with the catalysis of a given reaction. Nevertheless, the reconstruction of GPRs still remains a largely manual and time consuming process. Aiming at fully automating the reconstruction process of GPRs for any organism, we propose the open-source python-based framework GPRuler. By mining text and data from 9 different biological databases, GPRule

SUBMITTER: Di Filippo M 

PROVIDER: S-EPMC8601613 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature