splitting and storing in string to use in sql command

i have id and program_name
like 1  abc
     2 xyz
     3 pqr
on selection of programs i am storing data in database as ~1~3(if 1 and 3 is selected)
what i want to do now is that i want to write a query where program id not in(1,3)

since when i am retrieving data from database, i am getting data as ~1~3 and after splitting the data i am storing it in array but how can i use that with sql query with not in command