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Gap filling software tools | Pathway analysis

Gap filling for the reconstruction of metabolic networks is to restore the connectivity of metabolites via finding high-confidence reactions that could be missed in target organism.Source text:(Liu et al., 2017) DEF: an automated dead-end filling…
Meneco
Desktop

Meneco

Allows users to proceed topological gap-filling of genome-scale draft metabolic…

Allows users to proceed topological gap-filling of genome-scale draft metabolic networks. Meneco uses an Answer Set Programming (ASP) to considerer gap-filling as a qualitative combinatorial…

DEF
Web

DEF Dead-End Filler

A webserver aimed at aiding the gap filling step by finding the most biological…

A webserver aimed at aiding the gap filling step by finding the most biological meaningful candidate reactions in the metabolic network reconstruction. DEF constructs an endosymbiosis-resembling…

MIRAGE
Desktop

MIRAGE MetabolIc Reconstruction via functionAl GEnomics

Identifies missing network reactions by integrating metabolic flux analysis and…

Identifies missing network reactions by integrating metabolic flux analysis and functional genomics data. To reconstruct a metabolic network model for an organism of interest, MIRAGE starts from a…

fastGapFill
Desktop

fastGapFill

A scalable algorithm capable of detecting and filling network gaps in…

A scalable algorithm capable of detecting and filling network gaps in compartmentalized genome-scale models. fastGapFill draws on, and extends, fastcore, an algorithm to approximate the cardinality…

Likelihood-base…
Web
Desktop

Likelihood-based gap filling

Incorporates genomic evidence into the decision-making process for gap filling…

Incorporates genomic evidence into the decision-making process for gap filling reactions. Likelihood-based gap filling both maximizes the consistency of gap filled reactions with available genomic…

GrowMatch
Desktop

GrowMatch

An optimization-based framework for reconciling in silico/in vivo growth…

An optimization-based framework for reconciling in silico/in vivo growth predictions. GrowMatch reconciles GNG predictions (by suppressing functionalities in the model) and NGG predictions (by adding…

OMNI
Desktop

OMNI Optimal Metabolic Network Identification

Determines the active reactions in a genome-scale metabolic network based on a…

Determines the active reactions in a genome-scale metabolic network based on a limited number of experimentally measured fluxes. OMNI allows efficient identification of the set of reactions that…

GapFill
Desktop

GapFill

An optimization procedure that proceeds to fill gaps identified by GapFind by…

An optimization procedure that proceeds to fill gaps identified by GapFind by making the minimal number of modifications to the metabolic model. GapFill attempts to correct them using one or more of…

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