Difference between revisions of "Gap-filling-gapfilling solution with meneco draft medium"

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(Created page with "{{#ask: Category:Metabolite | ?common name | ?consumed by | ?produced by | ?consumed or produced by }}")
 
(Created page with "== TISOGEM description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == The automatic reconstruction of ''Tisocrysis_lutea'' results to a Genome scal...")
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{{#ask: [[Category:Metabolite]]
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== TISOGEM description ==
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| ?common name
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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| ?consumed by
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The automatic reconstruction of ''Tisocrysis_lutea'' results to a Genome scale Model containing 2796 reactions, 2745 metabolites, 2728 genes and 1212 pathways. This GeM was obtained based on the following sources:
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| ?produced by
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* Based on annotation data:
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| ?consumed or produced by
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
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}}
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*** Creation of a metabolic network containing 2568 reactions
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* Based on orthology data:
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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*** From template ''CREINHARDTII'' creation of a metabolic network containing: 558 reactions
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*** From template ''SYNECHOCYSTIS'' creation of a metabolic network containing: 260 reactions
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*** From template ''ATHALIANA'' creation of a metabolic network containing: 419 reactions
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*** From template ''ESILICULOSUS'' creation of a metabolic network containing: 1191 reactions
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* Based on expertise:
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*** 314 reaction(s) added
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* Based on gap-filling:
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** Tool: [https://pypi.python.org/pypi/meneco meneco]
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*** 17 reaction(s) added
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[[FILE:venn.png|frameless|border]]
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== Collaborative curation ==
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* Suggest reactions to add or remove:
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** Download this [[MEDIA:Add_delete_reaction.csv|from]]
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* Suggest new reactions to create and add:
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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* '''Follow the examples given in the form to correctly share your suggestions'''
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* Send the completed form(s) to: CONTACT_MAIL

Revision as of 18:40, 10 January 2018

TISOGEM description

Automatic reconstruction with AuReMe

The automatic reconstruction of Tisocrysis_lutea results to a Genome scale Model containing 2796 reactions, 2745 metabolites, 2728 genes and 1212 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: Pathway tools
      • Creation of a metabolic network containing 2568 reactions
  • Based on orthology data:
    • Tool: Pantograph
      • From template CREINHARDTII creation of a metabolic network containing: 558 reactions
      • From template SYNECHOCYSTIS creation of a metabolic network containing: 260 reactions
      • From template ATHALIANA creation of a metabolic network containing: 419 reactions
      • From template ESILICULOSUS creation of a metabolic network containing: 1191 reactions
  • Based on expertise:
      • 314 reaction(s) added
  • Based on gap-filling:
    • Tool: meneco
      • 17 reaction(s) added

Venn.png

Collaborative curation

  • Suggest reactions to add or remove:
  • Suggest new reactions to create and add:
  • Follow the examples given in the form to correctly share your suggestions
  • Send the completed form(s) to: CONTACT_MAIL
Retrieved from "http://gem-aureme.irisa.fr/tisogem/index.php?title=Gap-filling-gapfilling_solution_with_meneco_draft_medium&oldid=18962"