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Identification of Organisms Based on Analysis of Nucleotide Density Vectors
Maděránková, Denisa ; Babula, Petr (referee) ; Schwarz, Daniel (referee) ; Provazník, Ivo (advisor)
Most methods for analysis of genomic data work with symbolic sequences. Numerically represented genomic sequences can be analyzed by signal processing methods. A new method of numerical representation of DNA sequences, nucleotide density vectors, is proposed in this thesis. Usability of this method for purposes of molecular species identification is tested on DNA barcoding sequences. DNA barcoding is modern and popular methodology based on comparison of short mitochondrial DNA sequences. Beside species identification by proposed method based on nucleotide density vectors, higher taxa rank identification (e.g. families) was also tested. Furthermore, dendrograms were constructed from standardly used evolutionary distances and distances between nucleotide density vectors and the dendrograms were compared.
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Effect of different numerical representations of DNA on molecular taxonomy
Blaschová, Eliška ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This paper introduces the classical and molecular taxonomy used for classification of organisms. It represents the direction of DNA barcoding as a possibility to identify unknown organism. Acquired mitochondrial DNA sequences in DNA barcoding can by transform by suitable method to numerical representation that will properly inform about the organisms relationship to other taxa. In this work, we consider three methods of numerical representation: the 1st and 4th quadrant EIIP values and 3D numerical representation reduction. The practical part is programmed identification analysis, which assigns the test organisms reference organism. Testing is performed at 4 reference files and analyzed 5 files. The work summarized the success assigning the correct reference for the selected method of numerical representation.
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Effect of nucleotide density vector's reduction on molecular identification of organisms
Kosková, Markéta ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This work deals with the effect of nucleotide density vector's reduction on molecular identification of organisms. At the beginning of the theoretical part, the work explains the concept of species, its development and its mutations. The next section provides basics of taxonomy, particularly the molecular taxonomy and DNA barcoding, with a description of mitochondrial DNA and its usability in the identification of species. The end of the theoretical part provides information about the nucleotide density vectors which the practical part is focused on. Analysis of auxiliary values on nucleotide density vectors was accomplished in Matlab by evaluating 188 real DNA barcode sequences. The identification analysis of organism was performed with the best auxiliary value for 4 datasets of the reference barcode sequences and 5 datasets of analyzed sequences of same organisms. Afterwards, the evaluation of the analysis was done by using separate nucleotide density vectors of individual nucleotides and their amounts.
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Mitochondrial DNA for molecular taxonomy
Kalianková, Kateřina ; Babula, Petr (referee) ; Maděránková, Denisa (advisor)
This work deals with mitochondrial DNA and molecular taxonomy. Structure and composition of animal cell, deoxyribonucleic acids and mitochondrial ribonucleic acids are described in the introduction. Another part contains information of DNA barcoding and numerical representation of genomic sequences. Programs are described in the practical part.
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Determination of gastropods of the genus Radix, the intermediate hosts of trematodes
Mikešová, Kateřina ; Beran, Luboš (referee)
Lymnaeid snails of the genus Radix are common freshwater molluscs of Europe. Formerly, the following species have been reported from the Czech Republic according to the morphology of the shell: R. auricularia, R. peregra, R. ovata and R. ampla. However, recent studies involving molecular data revealed that species determination based on traditional approaches employing morphology of the shell and gonads can be more complicated, confusing and not fully reliable. The shape of the shell is affected by particular life conditions of the snails and proves to be highly variable. The characteristics that can be found on gonads are dependent on the reproductive phase of the snail, and sometimes also on the presence of trematode larval stages, which can cause parasitic castration. Recently, molecular taxonomy is the most reliable approach, especially when a combination of sequences of mitochondrial and nuclear DNA is used. As molecular analyses are relatively time-consuming and expensive, some authors try to find some additional morphological features that could be used for determination of Radix snails in the field, without the need of demanding equipment. Problems in taxonomy and systematics of members of the genus Radix have a practical point in studies of trematode life cycles. From the view of human and...
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Effect of different numerical representations of DNA on molecular taxonomy
Blaschová, Eliška ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This paper introduces the classical and molecular taxonomy used for classification of organisms. It represents the direction of DNA barcoding as a possibility to identify unknown organism. Acquired mitochondrial DNA sequences in DNA barcoding can by transform by suitable method to numerical representation that will properly inform about the organisms relationship to other taxa. In this work, we consider three methods of numerical representation: the 1st and 4th quadrant EIIP values and 3D numerical representation reduction. The practical part is programmed identification analysis, which assigns the test organisms reference organism. Testing is performed at 4 reference files and analyzed 5 files. The work summarized the success assigning the correct reference for the selected method of numerical representation.
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Effect of nucleotide density vector's reduction on molecular identification of organisms
Kosková, Markéta ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This work deals with the effect of nucleotide density vector's reduction on molecular identification of organisms. At the beginning of the theoretical part, the work explains the concept of species, its development and its mutations. The next section provides basics of taxonomy, particularly the molecular taxonomy and DNA barcoding, with a description of mitochondrial DNA and its usability in the identification of species. The end of the theoretical part provides information about the nucleotide density vectors which the practical part is focused on. Analysis of auxiliary values on nucleotide density vectors was accomplished in Matlab by evaluating 188 real DNA barcode sequences. The identification analysis of organism was performed with the best auxiliary value for 4 datasets of the reference barcode sequences and 5 datasets of analyzed sequences of same organisms. Afterwards, the evaluation of the analysis was done by using separate nucleotide density vectors of individual nucleotides and their amounts.
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Mitochondrial DNA for molecular taxonomy
Kalianková, Kateřina ; Babula, Petr (referee) ; Maděránková, Denisa (advisor)
This work deals with mitochondrial DNA and molecular taxonomy. Structure and composition of animal cell, deoxyribonucleic acids and mitochondrial ribonucleic acids are described in the introduction. Another part contains information of DNA barcoding and numerical representation of genomic sequences. Programs are described in the practical part.
|
|
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Identification of Organisms Based on Analysis of Nucleotide Density Vectors
Maděránková, Denisa ; Babula, Petr (referee) ; Schwarz, Daniel (referee) ; Provazník, Ivo (advisor)
Most methods for analysis of genomic data work with symbolic sequences. Numerically represented genomic sequences can be analyzed by signal processing methods. A new method of numerical representation of DNA sequences, nucleotide density vectors, is proposed in this thesis. Usability of this method for purposes of molecular species identification is tested on DNA barcoding sequences. DNA barcoding is modern and popular methodology based on comparison of short mitochondrial DNA sequences. Beside species identification by proposed method based on nucleotide density vectors, higher taxa rank identification (e.g. families) was also tested. Furthermore, dendrograms were constructed from standardly used evolutionary distances and distances between nucleotide density vectors and the dendrograms were compared.
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