Hi Amruta , you can use avaialble epitope prediction servers. First submit your original 27 aa region and look for predicted epitiopes, later submit your mutated 27aa region( if the region involves point mutation) and comapre there scores. You can use IEDB or SYPETHI .

Hello Amruta Naik

Firstly you have a choice of selecting the type of epitopes, frm CTL epitopes, HTL epitopes, B cell epitopes, IFN epitopes or even all of them. Look for the epitopes present in the original sequence, and as Vikash Kumar pointed out, compare their scores and choose the one with higher scores. Higher the score is, more is the efficiency of the epitopes to evoke the desired immune response.

You can use the following tools for predicting different antigenic epitopes from your sequence.

T cell epitopes:

http://tools.iedb.org/mhci/

http://tools.iedb.org/mhcii/

B cell epitopes:

http://crdd.osdd.net/raghava/abcpred/

http://tools.iedb.org/ellipro/

Interferon inducing epitopes:

http://crdd.osdd.net/raghava/ifnepitope/

Interleukin inducing epitopes:

https://webs.iiitd.edu.in/raghava/il10pred/algo.php

Hope it helps.