Analýza lidského genomu

Abstract

This thesis describes the implementation of suffix automatons used for string searching on long DNA sequences. The first chapter talks about DNA sequencing and mapping. Then follows a~theoretic primer on the topic of suffix trees and suffix arrays which are widely used for searching over long strings. The next chapter introduces suffix automatons, which are followed by compact suffix automatons, design draft and implementation of this structure. The implementation focuses on splitting the input string into several substrings, where for each substring a suffix automaton is constructed. A~wide number of experiments have been conducted over this data structure. Finally, the results from various experiments are summed up in the closing section.