A Mismatch Relaxation to the Primer Selection Process of an Amplicon Sequencing Algorithm

Bachelor thesis (2024)

Authors

D. Polimac Electrical Engineering, Mathematics and Computer Science

Contributors

J.A. Baaijens Pattern Recognition and Bioinformatics - EEMCS (mentor)
J. van Bemmelen Pattern Recognition and Bioinformatics - EEMCS (mentor)
C.A. Raman Pattern Recognition and Bioinformatics - EEMCS (graduation committee member)
Faculty
Electrical Engineering, Mathematics and Computer Science, Electrical Engineering, Mathematics and Computer Science
Copyright: © 2024 Dean Polimac
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Published Date

02-02-2024

Language

English

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Faculty

Electrical Engineering, Mathematics and Computer Science

Abstract

In this study we introduce a different approach to the primer selection problem in the AmpliDiff [12] algorithm. Two different metrics, being the Hamming distance [2], and the Levenshtein distance [4], are used to compute sets of similar primers. This is done such that locations where mismatches between the primers and the target sequence can occur are determined by the locations of similar primers. The impact that said mismatches have on the solution set of amplicons and their respective primers is outlined. With this we show potential benefits of allowing mismatches to occur, as well as their drawbacks.