Chromosomal DNA Barcode Assembly Using Hierarchical Clustering Matrix Method: Including Elastic Matching

Abstract: Obtaining DNA sequences is a time-consuming task, which typically requires one or several days for completion. One way of reducing analysis times is to be satisfied with long-range sequence patterns on the order of thousands of base pairs. DNA barcoding is a DNA-characterising technique that works according to this principle. It does so by using fluorescence microscopy to visualise long-range sequence patterns along DNA molecules which are fluorescently stained. The resultant light intensity curve works as an often unique identifier and is called a DNA barcode. This would be sufficient for identifying many bacteria species and would also provide a faster result compared to other candidate methods, with possible implementations in bacteriology, diagnosis and epidemiology. When DNA is to be extracted from cells, it breaks at some points along the way, resulting in DNA fragments. This happens even with the most sophisticated methods to date. Therefore, a computational part of the assembly process is required in order to obtain an intact DNA barcode. This thesis explores the addition of stretching out the fragments in the assembly process, to see to what extent it increases the assembly quality, as compared to a previous method [Wensi Zhu, Lund University, 2018]. Stretching as a parameter is motivated by the fact that confined DNA fragments in nano-channels are not equally stretched. In the assembly, we merge the fragments based on their similarity at different overlap and in a hierarchical order, always merging the best matching pair first. Comparing stretching to non-stretching, we found that the number of merged fragments and the size of DNA that it covers increases considerably with stretching included in the assembly process. It is therefore well motivated to include stretching in further analyses of DNA barcode assembly, in the ambition of developing DNA barcoding further.