Date of Award
Master of Science
Metagenomics is a study of DNA collected from the environmental samples in order to understand microbial taxonomy and their functional capabilities. Taxonomic profiling, which is to identify and quantify the abundances of microbial genomes in metagenomic samples, is one of the most important and challenging problem is analyzing metagenomic data. An alignment-based method requires alignment of reads from metagenomic samples to reference genomes and can be computationally expensive and time-consuming since microbial communities usually consist of hundreds to thousands of environmental microbial species. In this work, we introduce an efficient alignment-free method that creates an index of microbial genomes using Genomic Specific Marker, which is a marker that occurs uniquely in one genome or specifically in a group of genomes and is used to specifically represent a genome. The index will be used to estimate abundances in the metagenomic samples. In a controlled study at different levels of contamination, our method was able to achieve higher accuracy compared to current alignment-free methods in estimating abundances of species with very competitive running time.
dissertation or thesis originally submitted to the local University of Memphis Electronic Theses & dissertation (ETD) Repository.
Pham, Diem-Trang, "An Alignment-free Method for Profiling Microbial Community Using Genomic Specific Markers" (2016). Electronic Theses and Dissertations. 1346.