I have the complete sequence of most variable genes e.g. HA and NA of influenza-B/ -A virus, gained by using the sequencing primers. After the alignment with international sequences available in NCBI Genbank, I found many variations in the deduced amino acid sequences. After getting all these variations, I want to find the antigenic sites in this protein sequence. How can this be done?
You could try : http://www.immuneepitope.org/
or a similar online epitope prediction program to start. But you will need to confirm these predictions with antibody screens such as ELISAs or inject the peptide into animals to generate reactive antibodies
Dr. Jerome, I am thankful to you for nice advise regarding my Query. If you have more suggestion then plz forward me.
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