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Homologous Gene Finding
Lýčková, Veronika ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
This diploma thesis deals with the description of homologous genes and molecular biological databases that are used for their search and allow comparison. Among the most important institutions that deal with data management and analysis, include the EBI, NCBI and CIB. For searching homologous genes is the most fundamental NCBI - National Center for Biotechnology Information. More attention is paid to the search algorithms of homologous genes such as BLASTN and PatternHunter. The practical part of this thesis is the implementation of the algorithm comparing two sequences and locating homologous genes. The comparison is made on the basis of the nucleotide sequence and amino acid sequence. The results generated from the program will be further compared with results from commercially available programs.
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Determination genetics differencies using alignment signal of biological sequences DNA
Trněný, Ondřej ; Provazník, Ivo (referee) ; Valla, Martin (advisor)
Biological sequences are constantly evolving so there are mutations, deletions and inserts. Because of need to classify these sequences and determine degree of their similarity have been developed aligment methods. For example Dot matrix or algorithms like Needleman-Wunsch and Smith-Waterman used for global and local alignment. These methods can be considered as conservative and are limited because it is assumed that although there have been changes during evolution they still preserve small distance between similar regions. Therefore number of methods have been proposed to eliminate these limitations by comparing sequences without alignment. These methods for example Words in sequences, Euklidean distance or Universal sequence maps are designed to eliminate limitations of alignment using methods.
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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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Determination genetics differencies using alignment signal of biological sequences DNA
Trněný, Ondřej ; Provazník, Ivo (referee) ; Valla, Martin (advisor)
Biological sequences are constantly evolving so there are mutations, deletions and inserts. Because of need to classify these sequences and determine degree of their similarity have been developed aligment methods. For example Dot matrix or algorithms like Needleman-Wunsch and Smith-Waterman used for global and local alignment. These methods can be considered as conservative and are limited because it is assumed that although there have been changes during evolution they still preserve small distance between similar regions. Therefore number of methods have been proposed to eliminate these limitations by comparing sequences without alignment. These methods for example Words in sequences, Euklidean distance or Universal sequence maps are designed to eliminate limitations of alignment using methods.
|
|
|
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.
|
|
|
Homologous Gene Finding
Lýčková, Veronika ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
This diploma thesis deals with the description of homologous genes and molecular biological databases that are used for their search and allow comparison. Among the most important institutions that deal with data management and analysis, include the EBI, NCBI and CIB. For searching homologous genes is the most fundamental NCBI - National Center for Biotechnology Information. More attention is paid to the search algorithms of homologous genes such as BLASTN and PatternHunter. The practical part of this thesis is the implementation of the algorithm comparing two sequences and locating homologous genes. The comparison is made on the basis of the nucleotide sequence and amino acid sequence. The results generated from the program will be further compared with results from commercially available programs.
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