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Ambiguous representation of genetic variants in the VCF format
Neitzert, Gesa-Maret ; Daněček, Petr (advisor) ; Fišer, Karel (referee)
The variant call format (VCF) is a file format used to represent and store information about DNA variation. Genetic variants in VCF can be represented in multiple ways because the VCF specification allows for ambiguity, which can arise because of different variant calling pipelines or differences in sequence alignment. Ambiguities interfere with the comparison of VCF files and the variants therein, leading to complications in further analysis of variants. This thesis explores the differences in the representation of genetic variants that can occur, as well as their causes and impacts on further analysis. Furthermore, the normalization of VCF files is addressed and an algorithm for the atomization and deatomization of VCF files is shown. Keywords: VCF, variant call format, ambiguous variant representation, variant comparison, variant atomization, variant deatomization
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Molecular characterisation of novel subtype of Acute lymphoblastic leukemia with lineage switch during early phase of treatment
Dobiášová, Alena ; Fišer, Karel (advisor) ; Novotný, Marian (referee)
Leukemia is the most common malignant disease in children patients. In our laboratory (CLIP) a novel subtype of B-cell precursor Acute Lymphoblastic Leukemia (BCP-ALL) with lineage switch during early phase of treatment towards myeloid lineage (swALL) was recently documented. SwALL incidence is almost 4 % of all BCP-ALLs (Slámová et al., 2014). DNA methylation (presence of 5-methylcytosine) is together with post-translational histone modifications and non- coding RNAs an epigenetic mechanism which regulates gene expression without changes of genetic code. DNA methylation is easily detected by bisulphite conversion and subsequent sequencing. The aim of this work was to compare genome-wide DNA methylation patterns between patients with swALL and control BCP-ALLs. The first step in achieving that was revision and improvement of bioinformatic processing protocol for eRRBS data from massive parallel sequencing. To improve the sequence adapter trimming I tested four bioinformatic tools - FAR, cutadapt, Trimmomatic and fastx_clipper. I implemented the fastest and most effective - Trimmomatic into the processing protocol. As a next step I analysed the data with improved protocol and extended the analysis in R programming environment where the comparison of studied groups was performed. The comparison of...
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In silico prediction of postranslational modifications
Basíková, Iveta ; Novotný, Marian (advisor) ; Fišer, Karel (referee)
Post-translational modifications are an important form of cellural regulation, including matabolism, growth, differentiation, transcription activation, membrane transport and cell death. Experimental identification of post-translational modifications (PTMs), especially phosporylation, is still time consuming and expensive. Progress in silico PTM prediction tools was influnced an enormous growth of known sequences which are suitable for training set, processing and final result's interpretation. In silico prediction may facilitate the identification of potencional phosporylation sites and it may speed up in future research.
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A modern implementation of LALR(1) parser generator
Fišer, Karel ; Bednárek, David (advisor) ; Hnětynka, Petr (referee)
The goal of this thesis is to design and implement a modern parser generator. The result is a program that reads description of some context-free LALR(1) grammar and semantic actions from an input file. To output files the program generates source codes in several target modern object-oriented programming languages for implementation of the syntax analyzer which, when parsing the language corresponding to the given grammar, executes the given semantic actions. Powered by TCPDF (www.tcpdf.org)
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Bombic 2
Fišer, Karel ; Jelínková, Eva (referee) ; Lidický, Bernard (advisor)
Title: Bombic 2 Author: Karel Fišer Department: Department of Applied Mathematics Supervisor: RNDr. Bernard Lidický Supervisor's E-mail address: bernard@kam.mff.cuni.cz Abstract: The aim was to analyze the shortcomings of the first version of the game Bombic and to desing game and map editor removes these deficiencies. This concept then implement and create a programming and user documentation. As a result of the work originated programming piece, which consists of two programs. In the chapters of this work I describe in details the shortcomings of the first version, design of data storage and architecture of both programs. In chapter 6. I bring the user documentation. Read here how to install the programs, how to set up and play the game. I'm describing how to work with the map editor and how to create a new map. Keywords: Bombic, side-scrolling, arcade game, deathmatch
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Feedeng mixture bin
Frydrych, Martin ; Fišer, Karel (referee) ; Škopán, Miroslav (advisor)
This diploma thesis deals with proposal and construction of feeding mixture bin in two variants. The variant No. 1 has a capacity 53m3 with hopper angle 60° and the variant No. 2 has a capacity 45m3 with hopper angle 45°. The proposal of both variants of feeding mixture bin was worked out according to parameters of assignment and technical literature. Further it was made a calculation of wind load, snow load and a power reacting on bearing structure of bin in direction of thoroughfare. Technical documentation consists of configurations variant No. 1 and 2, chosen welding subassemblies and details of parts of variant No. 1 of feeding mixture bin.
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