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mapping interactions of proteins from two different species

Posted: Thu Jun 12, 2014 8:54 pm
by bubblepig
Hi all,

I would like to plot potential interactions of proteins from two bacterial species.
String-db only allows one species/query under protein mode.
Does anyone have any suggestions?


Posted: Mon Jun 16, 2014 6:18 pm
by ranio
In StringDB you can analyse species and export the interaction data respectively, and plot the interactions figure with different colours or shapes in Cytoscape.

In otherwise, you can try Dapple,

DAPPLE stands for Disease Association Protein-Protein Link Evaluator. DAPPLE looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature. The hypothesis behind DAPPLE is that causal genetic variation affects a limited set of underlying mechanisms that are detectable by protein-protein interactions. Please refer to the DAPPLE publication for full details.