How do I start DomainGraph and what can I do in DomainGraph?

Answer: DomainGraph can be started independently of AltAnalyze or through AltAnalyze. To start DomainGraph outside of AltAnalyze, open the folder AltAnalyze_v1release/Cytoscape_v2.6.1 and select the Cytoscape executable for your operating system. Within AltAnalyze, once you have completed an alternative exon analysis, the AltAnalyze results menu will appear:

From this menu, choose "Start DomainGraph in Cytoscape":

Once open, follow these directions, starting with Installing the DomainGraph database.