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Application for Alignment of DNA Parts
Kašpárek, Tomáš ; Žák, Jakub (referee) ; Rozman, Jaroslav (advisor)
This thesis deals with DNA sequences alignment methods with focus on execution speed of given task and its optimality. The outcome of this thesis results in multiple programs, which presents DNA alignment algorithms and their versions programmed with OpenCL libraries, which are optimized on calculation rate. Text of this thesis apprises reader with DNA alignment problematic and its importance in biology. Further, algorithms for DNA alignment and options of their speed-up using libraries like CUDA or OpenCL are presented.
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Hardware Acceleration of Algorithms for Approximate String Matching
Nosek, Ondřej ; Kořenek, Jan (referee) ; Martínek, Tomáš (advisor)
Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.
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Approximate String Matching Algorithm Implementation in FPGA
Pařenica, Martin ; Martínek, Tomáš (referee) ; Fučík, Otto (advisor)
This paper describes sequence alignment algorithms of nucleotide sequences. There are described pairwise alignment algorithms using database search or dynamic programming. Then in the paper is description of dynamic programming for multiple sequences and algorithm that builds phylogenetic trees. At the end of the first part of the paper is the description of technology FPGA. In the second part that is more practical is described implemntation of the choosen one algorithm. This part includes also examples of some multiple alignments.
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Detection of Dynamic Network Applications
Burián, Pavel ; Drahošová, Michaela (referee) ; Kaštil, Jan (advisor)
This thesis deals with detection of dynamic network applications. It describes some of the existing protocols and methods of their identification from IP flow and packet contents. It constitues a design of a detection system based on the automatic creation of regular expressions and describes its implementation. It presents the created regular expressions for BitTorrent and eDonkey protocol. It compares their quality with the solution of L7-filter.
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