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Optimization of Algorithms for Triplex Detection

By Jiří Hon

Abstract

Triplex-forming DNA sequences have been implicated as important players in several key processes, such as transcriptional regulation, DNA recombination and mutagenesis, which emphasize their importance for biology, biotechnology and medicine. This bachelor thesis optimizes recently publicated dynamic programming algorithm for identification of triplex-forming sequences on three levels of design: user interface, memory usage and computation time. On the level of user interface, the algorithm was extended with existing visualization functions and rewritten into R/Bioconductor package. Memory usage optimization and processor cache analysis in combination with computation time reduction based on current computation state analysis lead to more than three times acceleration

Topics: visualization; DNA; optimization; vizualizace; searching; vyhledávání; triplex; Bioconductor; R; identification; optimalizace; H-DNA; identifikace
Publisher: Vysoké učení technické v Brně. Fakulta informačních technologií
Year: 2013
OAI identifier: oai:invenio.nusl.cz:237779
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