Entering edit mode
7.5 years ago
kerstin.ha
•
0
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.
do you mean that you would like to map the protein into a pathway?
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.
question edited. hope it's understandable now XD
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.