Is it possible for a cs undergrad like me to apply for a cs grad program and study computational biology? I want to apply for an MS CS degree. However I want to study computational biology along with other subjects like AI, etc.
But many colleges have a separate department for computational biology(eg CMU) while others provide some courses to grad students of the cs department(eg Stanford).
Is it possible for me study computational biology at colleges which offer it as a separate program altogether?
I suggest that you make contact with the admissions of the target faculty, as well as make contact with academics whose research interests match the field you are interested in.  Have a look at the academic's profile pages as well as looking at papers that they may have published.

As JeffE said in his comment - why not?  You have computational background and a clear interest.