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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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Methods for multialignment of nucleotide sequences
Trněný, Ondřej ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
To be able to understand characteristics and purpose of biological sequences correctly, it is crucial to have a possibility to sort and compare them. Because of this need and to extend existing knowledge pool, numerous methods were proposed. Especially in field of multiple sequences alignment. Methods for multiple sequences alignment may provide various valuable information about sequences which failed to show enough similarity in pairwise alignment. According to this, several algorithms were implemented in various computer applications which provide a way to analyse huge sets of data. One of those, the progressive alignment algorithm, is implemented as a part of this thesis
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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.
|
|
|
Methods for multialignment of nucleotide sequences
Trněný, Ondřej ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
To be able to understand characteristics and purpose of biological sequences correctly, it is crucial to have a possibility to sort and compare them. Because of this need and to extend existing knowledge pool, numerous methods were proposed. Especially in field of multiple sequences alignment. Methods for multiple sequences alignment may provide various valuable information about sequences which failed to show enough similarity in pairwise alignment. According to this, several algorithms were implemented in various computer applications which provide a way to analyse huge sets of data. One of those, the progressive alignment algorithm, is implemented as a part of this thesis
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