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Assignment Rules not getting triggered when creating a case using Email Services

We are using Apex Email Services to create a case with the inbound emails.Every thing is working fine except the assignment rules. Case is not getting assigned based on the assignment rules.
Is there anything which im missing. Does email services support assignment rules? If it doesn't trigger, can any one please suggest a work around to trigger the assignment rules( with out writing the code for assignment in the apex class).
Any pointers will be of great help.
Thanks in advance