NeAT - Pathfinder

Do multiple-to-multiple end path finding. Click on help for help.
Web service and interface by Karoline Faust. This program calls REA (Jimenez and Marzal, 1999). See Credits for other contributors.

1. Network help



Enter the network here (tab-delimited* or gml):

*The tab-delimiter can be replaced by two white spaces.

Or upload the network from a file:


OR enter a network id (id of previously submitted network):


Comment on the demonstration example

The demo network is the union of all paths annotated for S. cerevisiae in BioCyc release 10.6. It is an undirected graph consisting of 2,656 edges.
The seed nodes are the start and end compound of the heme biosynthesis II pathway as annotated in BioCyc.
This pathway is one of the study cases described in Croes et al., J. Mol. Biol. 356: 222-236 (see our list of publications.)
Note that for this demo, path finding is done on a smaller, undirected graph without differentially weighting compounds and reactions (both receive a weight according to their degree). To find paths in directed metabolic networks with mutually exclusive reaction directions, check the advanced options of the Pathfinder tool. Use the Metabolic path finding tool to find paths in the complete KEGG network.
The path of first rank corresponds to the annotated heme biosynthesis II pathway. To see the influence of the weighting scheme, you can set the weighting scheme to unit weight and the rank to 1 (for quicker computation). You will obtain an entirely different result.



Input format 

Directed network
Store network on server


2. Seed nodes help



Info: Matching of provided identifiers to identifiers of nodes in the network is case-insensitive.

Enter source and target nodes:

Source nodes  
Target nodes

Or upload a batch file:



3. Path finding options help



Rank
Warning: The edge weight is seen as edge cost, not as edge strength!
Weighting scheme
Identifiers of nodes to exclude
Identifiers of nodes to include
Maximal path weight
Maximal path length
Minimal path length



4. Output help



Output format  

Table:
Graph:
       Graph format:       
       Graph output type:


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