Genetic information of all living organisms is stored in DNA. Exploring of its structure and function represents an important area of research in modern biology. One of the interesting structures occurring in DNA are palindromes. Based on the research they are expected to play an important role in interpreting the information stored in DNA, because they are often observed near important genes. Palindromes searching is complicated by the presence of mutations (changes in sequences of DNA elements), which increases the time complexity of algorithms. Therefore it is reasonable to study their parallelization and acceleration. The objective of this work is a study of palindromes searching methods and acceleration architecture design. The hardware unit implemented in a chip with FPGA technology placed on ml555 board can speed up the calculation up to 6 667 times in comparison with the best-known software method relying on suffix arrays.
| Identifer | oai:union.ndltd.org:nusl.cz/oai:invenio.nusl.cz:237194 |
| Date | January 2010 |
| Creators | Voženílek, Jan |
| Contributors | Kořenek, Jan, Martínek, Tomáš |
| Publisher | Vysoké učení technické v Brně. Fakulta informačních technologií |
| Source Sets | Czech ETDs |
| Language | Czech |
| Detected Language | English |
| Type | info:eu-repo/semantics/masterThesis |
| Rights | info:eu-repo/semantics/restrictedAccess |
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