title: fastGapFill: efficient gap filling in metabolic networks.
abstract: BACKGROUND
  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 the computation of biologically more relevant solutions. We demonstrate the efficiency and scalability of fastGapFill on a range of metabolic reconstructions.
  
  
  METHODS
  fastGapFill is freely available from http://thielelab.eu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, L-4362.
authors.forename: Ines
authors.initials: I
authors.lastname: Thiele
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, L-4362.
authors.forename: Nikos
authors.initials: N
authors.lastname: Vlassis
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, L-4362.
authors.forename: Ronan M T
authors.initials: RM
authors.lastname: Fleming
mesh_terms: D000465:Algorithms; D016678:Genome; D053858:Metabolic Networks and Pathways / Q000235:genetics; D012984:Software