Assignment Task
Immunology Prac 3. Bioinformatics
For your write-up of this practical, give an introduction on computational methods of epitope prediction (approx half a page), noting both T and B cell, and the differences. Answer the questions posed below in bold, with reasoning. You can answer within this document.
Introduction.
Write your introduction here.
Practical analyses.
1. Use the following sequence:
MGSIGAASMEFCFDVFKELKVHHANENIFYCPIAIMSALAMVYLGAKDSTRTQINKVVRFDKLPGFGDSIEAQCGTSVNVHSSLRDILNQITKPNDVYSFSLASRLYAEERYPILPEYLQCVKELYRGGLEPINFQTAADQARELINSWVESQTNGIIRNVLQPSSVDSQTAMVLVNAIVFKGLWEKTFKDEDTQAMPFRVTEQESKPVQMMYQIGLFRVASMASEKMKILELPFASGTMSMLVLLPDEVSGLEQLESIINFEKLTEWTSSNVMEERKIKVYLPRMKMEEKYNLTSVLMAMGITDVFSSSANLSGISSAESLKISQAVHAAHAEINEAGREVVGSAEAGVDAASVSEEFRADHPFLFCIKHIATNAVLFFGRCVSP
This peptide is widely used in antigen presentation assays in immunology.
Does another epitope predictor HYPERLINK “http://tools.immuneepitope.org/mhci/” \t “_blank” http://tools.immuneepitope.org/mhci/ also predict this as the dominant peptide in H2-kb mice?
Using the Hopp-Woods tool at https://web.expasy.org/protscale/ find the most hydrophilic region of the protein. Use the default window size (9). Where is it? Why might it be important to know this?
2. If you were going to design a peptide vaccine to (A) induce CTL’s, or (B) induce antibodies from the following sequence, which regions would you choose? Assume you will test in H2-Db mice.
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