You can follow the links below:-

1. http://bioware.ucd.ie/epic/

2. http://www.dnastar.com/t-sub-solutions-structural-biology-epitope-prediction.aspx

3. http://tools.immuneepitope.org/tools/bcell/iedb_input

ِDear Sandip,

Thank you very much

Dear Abdollah,

if you have an amino acid sequence and you search for T cell epitopes, try:

http://www.syfpeithi.de/bin/MHCServer.dll/EpitopePrediction.htm

Best wishes

Christoph

Dear Sandip

This is only for a protein: http://sysbio.unl.edu/SVMTriP/prediction.php

I suggest you always reach consensus when you use such tools.

Best

Prash