Metabolic Pathfinding supplement

This is the supplement for the article: "Metabolic Pathfinding Using RPAIR Annotation"

  1. Reference pathways
    The 116 reference pathways were obtained from the aMAZE database and can be downloaded in gdl format here. The gdl files can be loaded into Cytoscape with the CoNet app. For the display, the style "Directed" and the hierarchical layout are recommended. To differentiate compounds and reactions, the network style can be modified by mapping node shape to ObjectType with a discrete Mapper and selecting different shapes for compounds and reactions.
  2. Statistics on reference pathways and on path finding
  3. Metabolic Pathfinder web interface
    The web interface is available at NeAT tools. Open the sub menu Path finding by clicking the white triangle and select Metabolic path finding.
    Alternatively, the command line version of the pathfinding and pathway inference tools in NeAT can be downloaded from here.
  4. Metabolic networks
    The networks are available via the Metabolic Pathfinder web interface. Go to the Metabolic Pathfinder web interface, then click Manual and go to the KEGG graph repository. The Metabolic Pathfinder manual also provides information on the networks, under Graph type.
    Metabolic networks can also be downloaded from here.
  5. List of excluded compounds

KEGG version 41.0 has been used to generate the results.