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Epitope Mapping using Local Alignment Features
KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
2015 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Our immune system uses antibodies to neutralize pathogens such as bacteria and viruses. Antibodies bind to parts of foreign proteins with high efficiency and specificity. We call such parts epitopes. The identification of epitopes, namely epitope mapping, may contribute to various immunological applications such as vaccine design, antibody production and immunological diagnosis.

Therefore, a fast and reliable method that can predict epitopes from the whole proteome is highly desirable.


In this work we have developed a computational method that predicts epitopes based on sequence information. We focus on using local alignment to extract features from peptides and classifying them using Support Vector Machine. We also propose two approaches to optimize the features. Results show that our method can reliably predict epitopes and significantly outperforms some most commonly used tools.


Place, publisher, year, edition, pages
TRITA-MAT-E, 2015:51
National Category
Computational Mathematics
URN: urn:nbn:se:kth:diva-170658OAI: diva2:839498
Subject / course
Scientific Computing
Educational program
Master of Science - Computer Simulation for Science and Engineering
Available from: 2015-07-02 Created: 2015-07-02 Last updated: 2015-08-11Bibliographically approved

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