Applying Transition Matrix to Monitor the Shift Movement of Bases for Next Generation Sequencing Data

Abstract

As science develops the technology of DNA sequencing have progressed tremendously Understanding the serial order of nucleotides within a DNA molecule will be a great help to realize the whole genome expression and consequently make important breakthroughs in areas of medicine health science and others simultaneously Due to the variation of molecular structure the accuracy of base calling does raise the issue of in the quality of sequence assembly While the quality of base calling has been extensively investigated the shift movement of bases is relatively unexplored Several researches have been conducted and proved that the positions of bases are not fixed however the direction of shift movement has not been studied so far The purpose of this thesis focuses on monitoring the shift movement of bases for next generation sequencing (NGS) data from Illumina Miseq platform by using transition matrix The result of this study showed the existence of shifts over cycles and the shift movement direction could be detected by the transition matrix method

Date of Award	2016 Jun 28
Original language	English
Supervisor	Shih-Huang Chan (Supervisor)