|
|
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.
|
|
|
Analysis of animal mitochondrial genes for DNA barcoding
Brabencová, Klára ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The aim of this work is a literature review on the topic of the mitochondrial genome and DNA barcoding, building a dataset of mitochondrial sequences from GenBank database and creatione of a software function for extraction of individual genes that are present in the mitochondrial genome. This function was developed in Matlab. DNA barcoding is a method that uses short DNA sequence of mitochondrial genome for identification of species. There is no comprehensive work examining the appropriateness of different mitochondrial genes. This aim investigates the potential of other mitochondrial genes and evaluate their effectiveness for DNA barcoding and calculation of intra-and interspecific variability.
|
|
|
Design and Implementation of Sound Recognizer of Particular Grasshopper Species
Schwarz, Jan ; Peterek, Nino (advisor) ; Hlaváčová, Jaroslava (referee)
Biologists asked us to create a system that recognizes particular grasshopper species from stridulation records. Currently we recognize five grasshopper species which can be seen in the Czech Republic using a free available toolkit for speech recognition called HTK. In addition to the acoustic model itself we also created web sites, which would analyse a stridulation record and then save the result for subsequent utilization. The current model is based only on a limited amount of training records, but its results are satisfactory. The web sites also serve as a gathering system; consequently, it is possible to further extend and improve the model.
|
|
|
Design and Implementation of Sound Recognizer of Particular Grasshopper Species
Schwarz, Jan ; Peterek, Nino (advisor) ; Hlaváčová, Jaroslava (referee)
Biologists asked us to create a system that recognizes particular grasshopper species from stridulation records. Currently we recognize five grasshopper species which can be seen in the Czech Republic using a free available toolkit for speech recognition called HTK. In addition to the acoustic model itself we also created web sites, which would analyse a stridulation record and then save the result for subsequent utilization. The current model is based only on a limited amount of training records, but its results are satisfactory. The web sites also serve as a gathering system; consequently, it is possible to further extend and improve the model.
|
|
|
Molecular phylogeny of the genus Geosmithia
Korittová, Celie ; Kolařík, Miroslav (advisor) ; Tomšovský, Michal (referee)
The genus Geosmithia contains 11 described and several tens of undescribed species of fungi living nearly exclusively in galleries of subcorticolous insects, especially bark beetles. In this work, a phylogenetic analysis of the genus was made using DNA sequences of four protein-coding genes, namely TEF-1, RPB2, Mcm7 and Tsr1. The analysis has confirmed that ecological strategies of these fungi (such as association with conifers or broad leaved trees or symbiosis with ambrosia beetles) have evolved several times in this genus. 51 species are recognized based on the obtained phylogenetic tree according to Genealogical Concordance Phylogenetic Species Recognition. I have also tested utility of the above mentioned genes to serve as "barcode" for identification of closely related Geosmithia species.
|
|
|
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.
|
|
|
Analysis of animal mitochondrial genes for DNA barcoding
Brabencová, Klára ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The aim of this work is a literature review on the topic of the mitochondrial genome and DNA barcoding, building a dataset of mitochondrial sequences from GenBank database and creatione of a software function for extraction of individual genes that are present in the mitochondrial genome. This function was developed in Matlab. DNA barcoding is a method that uses short DNA sequence of mitochondrial genome for identification of species. There is no comprehensive work examining the appropriateness of different mitochondrial genes. This aim investigates the potential of other mitochondrial genes and evaluate their effectiveness for DNA barcoding and calculation of intra-and interspecific variability.
|
|
|
Application of DNA barcoding on genus \kur{Folsomia} (Collembola) and mitochondrial geonome of \kur{F. candida}
SLÁMOVÁ, Martina
Mitochondrial molecular marker COI was tested for use in species identification of selected species of genus Folsomia (Collembola). Marker was succesfuly amplified and sequenced. Dendrogram constructed by Neighbor-Joining method with Kimura-2-Parameter model grouped all individuals into presumed species clusters and high intraspecific variability of F. quadrioculata suggests the existence of cryptic species. Furthermore, 65 % of mitochondrial geonome of F. candida was obtained with 16 tRNA genes, 9 proteincoding genes and 2 rRNA genes identified. So far the genome characteristics correspond to the one described in G. hodgsoni.
|
|
|
Species identification and molecular taxonomy of gallmidges (\kur{Cecidomyiidae})
STROUHALOVÁ, Renata
Four molecular markers were tested for their potential to be used for species identification of selected taxa of Cecidomyiidae. Two markers were succesfully amplified, part of the mitochondrial COI ({\clqq}DNA barcoding`` marker) and nuclear fragment ITS1. Subsequent analysis of their intra- and interspecific variability enabled us to resolve several taxonomical uncertainties. However, both markers appear to be too variable for reliable delineation of species and genera under investigation.
|
guest ::
