I want to find the Transmembrane domains in a sequence of protein. The number of transmembrane domains displayed by various tools differs. I have used TOPCONS, OCTOPUS, etc. Is there a tool in which I can force the output to give the desired number of transmembrane domains?
You could try CCTOP. It allows you to specify additional constraints, after the prediction is complete, click customize. There you can add additional custom constraints at the bottom of the page (click the Additional +), and specify the topology type and location, and recalculate.
TOPDB is a database of transmembrane proteins and annotated topology, where you can apply a search filter on the number of transmembrane domains.