Optimization based automated curation of metabolic reconstructions.

ABSTRACT:

Background

Currently, there exists tens of different microbial and eukaryotic metabolic reconstructions (e.g., Escherichia coli, Saccharomyces cerevisiae, Bacillus subtilis) with many more under development. All of these reconstructions are inherently incomplete with some functionalities missing due to the lack of experimental and/or homology information. A key challenge in the automated generation of genome-scale reconstructions is the elucidation of these gaps and the subsequent generation of hypotheses to bridge them.

Results

In this work, an optimization based procedure is proposed to identify and eliminate network gaps in these reconstructions. First we identify the metabolites in the metabolic network reconstruction which cannot be produced under any uptake conditions

SUBMITTER: Satish Kumar V 

PROVIDER: S-EPMC1933441 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature