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Bioinformatics of human genome
Kupková, Karolína ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with DNA segments containing only adenine and guanine. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There are basic informations about chimpanzees and the human genome and conformations of the chains containing adenine with guanine. The practical part consists of a program that searches for the required sections in sequence, it displays and saves it. The thesis includes analysis of genes which are common for humans and chimpanzees, which were analyzed to determine randomness, functionality a preserving of these sections.
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Similarity/dissimilarity analysis of genomic data on the basis of graphical representation
Těthal, Jiří ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The work deals with the identification of species of animal through the density of nucleotids of mitochondrial gene CO1. In the first part the theory summarized information about DNA barcoding and the mitochondria, cellular organel that with this method is closely related. The second part deals with virtually comparing different sequences using the density of nucleotides. For this it was created program, which uses two functions, the first of the specified nucleotide sequence calculates the density and one can compare the density by distance methods.
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Character-based methods for DNA barcoding
Kalianková, Kateřina ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This work deals with character-based DNA barcoding. DNA barcoding and character-based DNA barcoding methods are described in the introduction. Another part contains information of method CAOS (Characteristic Attributes Organization) and method BLOG (Barcoding with LOGic). Programs are described in the practical part. The end contains results.
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Techniques for Comparing Biological Sequences
Sladký, Roman ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
This work presents the building up of basic biological units DNA, RNA and proteins as well as their function. Provided data are kept in biological databases which are connected worldwide to supply preferable communication along with all kinds of available information to be used in the scientific research. The secret of alive is hidden in genes coded in sequences of nucleotides. Genes enable the creation of proteins which are made of sequences of amino-acids. The wide-spread methods of comparing these sequences are FASTA and BLAST algorithms. Their base is used for the PSProt program which is described in this work. PSProt program is the tool for comparing the sequences of proteins. First it is necessary to synthesise the protein from the DNA oligonucleotide because it codes the surveyed protein. The most similar proteins are searched out by heuristic of hitpoints, then their final score that is essential for aligning is modified by semiglobal alignment algorithm.
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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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Genomic Data Mining Techniques
Jaša, Petr ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
First of all, this thesis sets itself a goal to introduce some common technics for datamining in genomics and as a next step to implement own algorithm like algorithm BLAST. In the concrete, this work is pointed to sequences of DNA. The DNA sequence contains in itself genetic information, which is template for living organism. For explanation this information can be used number of technics. This paper describes algorithm Fasta and algorithms from BLAST family. With these algorithms, it is possible to gain a lot of important information even about such DNA sequences, where only primary structure is known. Principle of these algorithms is based on alignments of one query sequence, which we want to obtain some information from, with many sequences stored in database. According to result alignment, it is possible to determine many features of the query sequence.
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Character-based methods for DNA barcoding
Kalianková, Kateřina ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This work deals with character-based DNA barcoding. DNA barcoding and character-based DNA barcoding methods are described in the introduction. Another part contains information of method CAOS (Characteristic Attributes Organization), method BLOG (Barcoding with LOGic) and method BLAST. Programs are described in the practical part. The end contains results.
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Genomic Data Mining Techniques
Jaša, Petr ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
First of all, this thesis sets itself a goal to introduce some common technics for datamining in genomics and as a next step to implement own algorithm like algorithm BLAST. In the concrete, this work is pointed to sequences of DNA. The DNA sequence contains in itself genetic information, which is template for living organism. For explanation this information can be used number of technics. This paper describes algorithm Fasta and algorithms from BLAST family. With these algorithms, it is possible to gain a lot of important information even about such DNA sequences, where only primary structure is known. Principle of these algorithms is based on alignments of one query sequence, which we want to obtain some information from, with many sequences stored in database. According to result alignment, it is possible to determine many features of the query sequence.
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Character-based methods for DNA barcoding
Kalianková, Kateřina ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This work deals with character-based DNA barcoding. DNA barcoding and character-based DNA barcoding methods are described in the introduction. Another part contains information of method CAOS (Characteristic Attributes Organization), method BLOG (Barcoding with LOGic) and method BLAST. Programs are described in the practical part. The end contains results.
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