FastGapFill: efficient gap filling in metabolic networks.

ABSTRACT:

Motivation

Genome-scale metabolic reconstructions summarize current knowledge about a target organism in a structured manner and as such highlight missing information. Such gaps can be filled algorithmically. Scalability limitations of available algorithms for gap filling hinder their application to compartmentalized reconstructions.

Results

We present fastGapFill, a computationally efficient tractable extension to the COBRA toolbox that permits the identification of candidate missing knowledge from a universal biochemical reaction database (e.g. Kyoto Encyclopedia of Genes and Genomes) for a given (compartmentalized) metabolic reconstruction. The stoichiometric consistency of the universal reaction database and of the metabolic reconstruction can be tested for permitting th

SUBMITTER: Thiele I 

PROVIDER: S-EPMC4147887 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature