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Table 1 Software tools developed for genome-scale metabolic reconstruction

From: Toward the automated generation of genome-scale metabolic networks in the SEED

Steps

Purpose of Tools

Implementation in the SEED

Database Contributions

ANNOTATION

 

The SEED already provides tools for annotation, based on similarity searching and context-based methods

The SEED already provides a database of high-quality genome annotations organized into subsystems (see [11])

SUB-ASSEMBLY AND SUB-NETWORK VERIFICATION

Curating associations between functional roles and reactions in a particular metabolic context

Reverse-engineering of published genome-scale metabolic models; analysis of gene-reaction associations in the KEGG database; integrated display of KEGG pathway maps in subsystems, highlighting functional roles and associated reactions

Associations between functional roles and KEGG reactions in subsystems

 

Assembling and verifying the coherence of reaction subnetworks in subsystems

Petri net representation of KEGG reactions; encoded scenarios in subsystems; finding paths through reaction subnetworks from scenario inputs to scenario outputs

Reuseable coherent reaction subnetworks in subsystems

 

Assembling and verifying the coherence of connected reaction subnetworks across subsystems

Connections between scenarios in different subsystems; finding paths through connected scenarios, from overall inputs to overall outputs

List of curated subsystems with coherent reaction subnetworks for functional variants that interconnect to cover central and intermediary metabolic pathways

ASSEMBLY AND NETWORK VERIFICATION

Assembling and verifying the coherence and completeness of an organism-specific reaction network

Identifying gaps in the reaction network, by cross-checking inputs and outputs for all paths through implemented scenarios, and checking for paths from minimal substrates to biomass compounds; creating files for FluxAnalyzer [36]

Organism-specific complete and coherent reaction networks for central and intermediary metabolism