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Attacks on Cryptographic Modules
Daněček, Petr ; Zeman, Václav (advisor)
The conventional way of cryptanalysis is based on the cryptographic algorithms weak points examine. The attack model of conventional cryptanalysis covers mathematical description of the cryptographic algorithm used. This model is not with the relation to the physical model implementation and the real environment. Cryptographic algorithms currently used in the combination with strong cipher keys are almost unbreakable and the conventional cryptanalysis is ineffective. The new way of cryptanalysis employs the side channels. The model of cryptanalysis using side channels is enhanced with physical revelation of module performing the cryptographic operations. This dissertation thesis deals with cryptographic module description and studies influence of side channels to the security of this module.
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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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Limitations of variant consequence predictors
Břicháčková, Kateřina ; Daněček, Petr (advisor) ; Kolář, Michal (referee)
Thanks to numerous large-scale sequencing projects, the number of discovered genomic variants is increasing. The key step in analyzing the variant data is the functional annotation, since it helps researchers and clinicians to categorize, filter and prioritize the variants for further research. This thesis discusses five commonly-used variant consequence predictors, offers advice on how to use them and briefly goes through the algorithms they employ. Moreover, various data formats as well as the human reference genome and different genome annotations are described in the thesis. The correctness of the reference is of great importance as all the predictors rely on it. This thesis highlights some situations in which the results given by different predictors can vary. All the tests were made using the Ensembl gene annotation (release 92) and the GRCh38 reference assembly.
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Variant calling using local reference-helped assemblies
Dráb, Martin ; Daněček, Petr (advisor) ; Hoksza, David (referee)
Despite active development during past years, the task of sequencing a genome still remains a challenge. Our current technologies are not able to read the whole genome in one piece. Instead, we shatter the target genome into a large amounts of small pieces that are then sequenced separately. The process of assembling these small pieces together, in order to obtain sequence of the whole genome, is painful and rsource-consuming. Multiple algorithms to solve the assembly problem were developed. This thesis presents yet another assembly algorithm, based on the usage of de Bruijn graphs, and focusing on sequencing short genome regions. The algorithm is compared to well-known solutions in the field. 1
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Attacks on Cryptographic Modules
Daněček, Petr ; Zeman, Václav (advisor)
The conventional way of cryptanalysis is based on the cryptographic algorithms weak points examine. The attack model of conventional cryptanalysis covers mathematical description of the cryptographic algorithm used. This model is not with the relation to the physical model implementation and the real environment. Cryptographic algorithms currently used in the combination with strong cipher keys are almost unbreakable and the conventional cryptanalysis is ineffective. The new way of cryptanalysis employs the side channels. The model of cryptanalysis using side channels is enhanced with physical revelation of module performing the cryptographic operations. This dissertation thesis deals with cryptographic module description and studies influence of side channels to the security of this module.
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