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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