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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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Clustering of Protein Sequences Based on Primary Structure of Proteins
Jurásek, Petr ; Stryka, Lukáš (referee) ; Burgetová, Ivana (advisor)
This master's thesis consider clustering of protein sequences based on primary structure of proteins. Studies the protein sequences from they primary structure. Describes methods for similarities in the amino acid sequences of proteins, cluster analysis and clustering algorithms. This thesis presents concept of distance function based on similarity of protein sequences and implements clustering algorithms ANGES, k-means, k-medoids in Python programming language.
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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.
|
|
|
Clustering of Protein Sequences Based on Primary Structure of Proteins
Jurásek, Petr ; Stryka, Lukáš (referee) ; Burgetová, Ivana (advisor)
This master's thesis consider clustering of protein sequences based on primary structure of proteins. Studies the protein sequences from they primary structure. Describes methods for similarities in the amino acid sequences of proteins, cluster analysis and clustering algorithms. This thesis presents concept of distance function based on similarity of protein sequences and implements clustering algorithms ANGES, k-means, k-medoids in Python programming language.
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