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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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Analysis of GPS data in orienteering sports
Picek, Štěpán ; Gregor, Petr (advisor) ; Kučera, Petr (referee)
In orienteering sports, there are many analytical tools used for determining the performance of competitors and the visualization of the routes. However, none of these tools allows automatic comparison and subsequent analysis of competitors' completed track between each single control point. The thesis intends to use the Needleman-Wunsch bioinformatics algorithm for comparison of GPS data, and their visualization within a web application. The application allows comparison of the track with other competitors, analysis of the performance and the connection with other tools. It is created on the ASP.NET Core platform and the Model- View-Controller design pattern with the use of other technologies such as HTML, CSS and TypeScript.
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Determination of genetic differences of biological DNA sequences
Sliž, Ladislav ; Škutková, Helena (referee) ; Provazník, Ivo (advisor)
Work on determining the genetic diversity of biological signal aligning DNA sequences, will address a brief description of the composition of DNA. Following is basic information on the bioinformatics analysis. Then the work will describe the possibility of aligning DNA sequences. Work will focus primarily on global Needleman-Wunsch algorithm and local Smit - Watermanovův algorithm. Furthermore, this work will focus on aligning DNA sequences using methods CGR and FCGR. At the end of the work will describe the practical application of identifying genetic differences by aligning the sequences.
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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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