Web based application:
Application will be loaded in the server. Client machine use the application using URL. You have to test it on different web browsers. Web applications are supposed to be tested on different browsers and OS platforms so broadly Web application is tested mainly for browser compatibility and operating system compatibility, error handling, static pages, back end testing and load testing.
Window based application:
It runs on personal computers and work stations, so when you test the desktop application you are focusing on a specific environment.
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