UC Irvine

Motivated by the Smith-Waterman algorithm, this dissertation studies the problem of alignment on the DNA sequences. Traditional methods like the Smith-Waterman algorithm is applying classic dynamic programming on the DNA nucleotide sequences. However, they have several disadvantages. The first one is that the Smith-Waterman algorithm is utilizing the DNA nucleotide sequences to achieve the alignment and can only show how two sequences are aligned, not a finalized aligned sequence. And various parameters, the penalty for substitution, insertion, and deletion, designed by users could occur different alignment results. This work proposes the method of dynamic time warping(DTW) combined with Nanopore technology and base-calling technology to achieve a finalized aligned sequence and improve the base-calling accuracy. In particular, DTW, Nanopore technology, and guppy base-caller are utilized to the DNA strands and finally, we can show base-calling sequences with higher accuracy compared to the base-calling sequences without alignment. Simulation results can show that our soft information alignment can finalize the aligned sequences and improve the base-calling accuracy.