GapFill protocols

View GapFill computational protocol

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GapFill specifications


Unique identifier OMICS_13372
Name GapFill
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Costas Maranas <>

Publication for GapFill

GapFill in pipeline

PMCID: 3444828
PMID: 22997515
DOI: 10.1155/2012/323472

[…] incapable of a desired level of flux through the biomass reaction, have been previously proposed. gapfind [] is a procedure that determines which metabolites in a network cannot be produced, and gapfill [] determines a minimal set of reactions to add from a universal database so that a specified set of metabolites may be produced. these optimization-based procedures have already […]

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GapFill in publications

PMCID: 5877332
PMID: 29538350
DOI: 10.3390/s18030860

[…] was based on ccd images. the corrected root-mean-square error (rmse) was less than 0.5 pixels. in addition, due to the failure of the landsat-7 airborne scan line corrector (slc) in may 2003, gapfill processing was required for the etm+ images., daily meteorological data for the whole year, including temperature, daylight, precipitation, and solar radiation, was provided by the zhuzhou […]

PMCID: 5829631
PMID: 29527198
DOI: 10.3389/fmicb.2018.00296

[…] construction method is roughly divided into four steps: step 1: an automated genome-based construction with automated procedures and applying automated tools, such as smiley algorithm, gapfind/gapfill, and pathologic; step 2: construction of the trn based on bibliomic data or high-throughput data; step 3: transforming a genome-scale reconstruction of the interactions into a computational […]

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

[…] problems. to increase gap-filling speed, the current (november 2017) gap-filling algorithm provided by the modelseed website uses a modified version of the fastdev technique., the gapfind/gapfill [] applications use milp to find blocked metabolites and gap-fill a reaction network, respectively. gapfill uses kegg or metacyc as a source of candidate reactions to add to the reaction […]

PMCID: 5843367
PMID: 29300007
DOI: 10.1038/nature25140

[…] siv-infected hosts. we sequenced genomic dna to a whole-genome coverage of about 180× using the illumina hiseq 2000 platform, and produced an initial assembly using allpaths-lg, atlas-link and atlas-gapfill (see methods for details). the total size of the assembled c. atys genome (caty_1.0; ncbi accession number gca_000955945.1) is around 2.85 gb, with a contig n50 size of 112.9 kb and scaffold […]

PMCID: 5689209
PMID: 29145861
DOI: 10.1186/s12915-017-0439-6

[…] illumina hiseq 2000 instruments generating 100 bp pe reads. reads were assembled using allpaths-lg (v35218) [] and further scaffolded and gap-filled using in-house tools atlas-link (v.1.0) and atlas gapfill (v.2.2) ( atlas-link is a scaffolding or super-scaffolding method that utilizes all unused mate pairs to increase scaffold sizes and create new scaffolds […]

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GapFill institution(s)
Department of Industrial and Manufacturing Engineering, The Pennsylvania State University, University Park, PA, USA; Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
GapFill funding source(s)
This work was funded from the DOE grant (DE-FG03 01ER25499).

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