Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti.

ABSTRACT:

Background

Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed.

Results

We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connected through gap metabolites, is proposed. The method has been successfully applied to the curati

SUBMITTER: Ponce-de-Leon M 

PROVIDER: S-EPMC3819652 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature