| dc.description.abstract | Immunogenic epitopes in a polyepitope construct may induce immunity against multiple
antigenic targets only if epitopes are correctly processed and presented. Applications that
combine multiple supertypes and integrate variables that measure the quality of
polyepitopes can be used to make better polyepitopes yet there are no publicly accessible
tools. In this research project, the researcher developed a web-based polyepitope
optimization prototype. The prototype runs on 3-tier application architecture: MYSQL was
used for the database tier, PHP for the application tier that runs on Apache HTTP server
and the presentation layer was implemented on a web browser. The researcher collected
epitopes data and information from online databases; the Immune Epitope Database
(IEDB), HIV molecular immunological database and National Center for Biotechnology
Information (NCBI).The epitopes were analyzed using Microsoft Excel 2003 and uploaded
onto a local database. Polyepitopes were generated, optimized and tested on an online web
server NetChop 3.1 which was used to validate one of the polyepitope quality
measurement variables- proteasome cleavage predictions. The results of data analysis
indicate that the immune system recognize epitopes in clusters and the main clusters are 9mers(9
amino acid long), 15mers,20mers and 25mers.The polyepitope optimization results
indicate that polyepitope optimization algorithms that integrate proteasome cleavage
prediction, transporter associated with antigen processing (TAP) binding prediction and
Major Histocompatibility Complex (MHC) binding predictions can be used to develop
better polyepitopes which can be used to make better vaccines within a shorter time and at
a lower cost | en |
