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fastGapFill specifications

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Unique identifier OMICS_06010
Name fastGapFill
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Publication for fastGapFill

fastGapFill citations

 (3)
library_books

Evaluation of reaction gap filling accuracy by randomization

2018
BMC Bioinformatics
PMCID: 5813426
PMID: 29444634
DOI: 10.1186/s12859-018-2050-4

[…] and gap-fill a reaction network, respectively. gapfill uses kegg or metacyc as a source of candidate reactions to add to the reaction network such that a specific metabolite becomes unblocked., fastgapfill [] gap-fills a compartmentalized reaction network. it has been tested using the kegg database as a source of candidate reactions. its algorithm is based on lp and greedily expands a set […]

library_books

In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host

2017
Front Microbiol
PMCID: 5727896
PMID: 29276507
DOI: 10.3389/fmicb.2017.02440

[…] have adapted and expanded an existing host–microbe constraint-based metabolic model to allow for the possibility of cross-kingdom metabolite transport via omvs. by combining experimental data with fastgapfill (fgf) (), an algorithm for inferring missing reactions in incomplete metabolic networks, we have linked the observed metabolites in omvs to both the bt and mouse metabolic networks. […]

library_books

Discovering missing reactions of metabolic networks by using gene co expression data

2017
Sci Rep
PMCID: 5288723
PMID: 28150713
DOI: 10.1038/srep41774

[…] a summary of these methods. typically, gap analysis methods consist of two main steps. the first step is to find ‘imperfections’ of the network. a group of these methods, like gapfind/gapfill and fastgapfill, detect topological flaws of the network such as blocked reactions and dead-end metabolites. other gap finding methods try to find the inconsistencies between model predictions […]


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fastGapFill institution(s)
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg

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