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Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of SJAPGEM results to a Genome scale Model containing 3344 reactions, 3242 metabolites, 5022 genes and 1388 pathways. This GeM was obtained based on the following sources:

• Based on annotation data:
  • Tool: Pathway tools
    • Creation of a metabolic network containing 2560 reactions
• Based on orthology data:
  • Tool: Pantograph
    • From template NANNOCHLOROPSIS_SALINA creation of a metabolic network containing: 595 reactions
    • From template ARABIDOPSIS_THALIANA creation of a metabolic network containing: 425 reactions
    • From template ECTOCARPUS_SILICULOSUS creation of a metabolic network containing: 1498 reactions
• Based on expertise:
  • • 74 reaction(s) added
• Based on gap-filling:
  • Tool: meneco
    • 90 reaction(s) added

Collaborative curation

• Suggest reactions to add or remove:
  • Download this form
• Suggest new reactions to create and add:
  • Download this form
• Follow the examples given in the form(s) to correctly share your suggestions
• Send the filled form(s) to: gabriel.markov@sb-roscoff.fr