mapping interactions of proteins from two different species
Posted: Thu Jun 12, 2014 8:54 pm
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
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, http://www.broadinstitute.org/mpg/dapple/dappleTMP.php#
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.