Detekce virových sekvencí při analýze exprese genů

Abstract

This Bachelor thesis deals with issues in the biomedical field of DNA/RNA sequencing and subsequent processing of the FASTQ file into a SAM file and its subsequent analysis and software creation tool. The software tool focuses on mapping the FASTQ file to reference viral sequences, filtering the SAM file, analyzing the SAM file, visualizing the results of the analysis, as well as working with the Blast API. By combining imperative, object oriented, and functional programming, I have created a software tool that is able to determine, using already known virus gene information, whether or not a virus is present in a sample of data. From my findings, it is necessary to perform a thorough analysis of the SAM file and take into account the coverage of the individual genes of all viruses found in the data sample. However, thanks to in-depth analysis, some of my results have suggested interesting conclusions. Part of the job is also the concrete process of using the developed software tool with analysis of the outputs of my tool.