Reference : FASTGAPFILL: Efficient gap filling in metabolic networks

	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Multidisciplinary, general & others
	To cite this reference:	http://hdl.handle.net/10993/17458

Title :	FASTGAPFILL: Efficient gap filling in metabolic networks
Language :	English
Author, co-author :	Thiele, Ines [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Vlassis, Nikos [> >]
	Fleming, Ronan MT [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Publication date :	2014
Journal title :	Bioinformatics
Publisher :	Oxford University Press - Journals Department
Volume :	30
Issue/season :	17
Pages :	2529-2531
Peer reviewed :	Yes (verified by ORBilu)
Audience :	International
ISSN :	1367-4803
e-ISSN :	1460-2059
City :	Oxford
Country :	United Kingdom
Abstract :	[en] 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 theidentification of candidate missing knowledge from a universal biochemical reaction database (e.g., KEGG) for a given (compart-mentalized) 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.
Research centres :	Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Machine Learning (Vlassis Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Systems Biochemistry (Fleming Group)
Permalink :	http://hdl.handle.net/10993/17458
DOI :	10.1093/bioinformatics/btu321
Other URL :	http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=24812336

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