Finally I have a Spam free (nearly) mailbox. I tried this utility DisSpam. What this does is as follows.
– It connects to a pop mailbox.
– Checks for spam emails by comparing with Spam Assassin (the best spam control tool).
– Deletes the spam mail from the server.
– Then you start your mail client and download only the clean messages.
To increase the effectiveness you can also train spamassassin in case it didn’t identified some mails as spam.
I also use another tool: popcheck which shows all your email header and lets you delete directly from the server.