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Shortest way between Protein and Pathway?

Hello

I'm looking for a tool that can give me the shortest path between a protein and a certain pathway. That could be any protein and it's not a part of the pathway. I would like to know the shortest interaction path of this protein to any member of the pathway. Does such a tool exist?

Thank you in advance.

shortest-path
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updated by Ram Ram • written by kerstin.ha • kerstin.ha

do you mean that you would like to map the protein into a pathway?

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written by dago dago

I think they mean what is the shortest pathway, via protein-protein interactions, between a Protein a and any protein that is in pathway B.

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written by i.sudbery i.sudbery

question edited. hope it's understandable now XD

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written by kerstin.ha • kerstin.ha

If you have a graph object (of your protein and the pathway), then you could convert it into a minimum spanning tree (MST) which will 'summarise' the graph into a single path. What you're asking may also be an implementation of the Travelling Salesman Problem (TSP). Take a look at the igraph package in R.

If it's a curated pathway, then maybe KEGG has some online tools, but I'm not sure.

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written by Kevin Blighe Kevin Blighe

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