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Searching for similar secondary structures in RNA
Vojtek, Daniel ; Mráz, František (advisor) ; Hoffmann, Petr (referee)
In contrast to DNA, the RNA strings fold into complicated secondary structures, which are highly important for their function. Main goal of this work was to create an application, which allows designing a detailed pattern of RNA secondary structure and then finding similar ones in the given set of RNA. The application has also direct access to GenBank database, from which it can download RNA sequences according to the user-defined query. Sequences without secondary structure are folded using a function from Vienna RNA Package. A part of the application is a graphic user interface, which provides comfortable way to design a pattern and allows the browsing found similar secondary structures. The work also presents basic principles of searching of similar RNA secondary structures and its usage in building phylogenetic trees. Description of all used algorithms is present too.
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Implementace paralelního zpracování dotazů v databázovém systému PostgreSQL
Vojtek, Daniel ; Štroffek, Julius (advisor) ; Bednárek, David (referee)
CONTENTS vi Title: Implementation of parallel query processing in PostgreSQL Author: Bc. Daniel Vojtek Department: Department of Software Engineering Supervisor: Mgr. Július Štroffek Supervisor's e-mail address: julo@stroffek.cz Abstract: Parallel query processing can help with processing of huge amounts of data stored in database systems. The aim of this diploma the- sis was to explore the possibilities, analyze, design and finally implement parallel query processing in open source database system PostgreSQL. I used a Master/Worker design pattern, in which standard PostgreSQL backend process is a master. As workers I used processes created from postmaster. In the thesis I focused on preparing an infrastructure nec- essary for parallel processing. I defined a new top level memory context over shared memory, which allows efficient and convenient memory al- locations. Then I implemented creation of new worker processes, based on master process requirements. To be able to control these workers I defined controlling structures using state machines. Then I implemented parallel sort operation and SQL operator UNION ALL using this infras- tructure. The result of this diploma thesis is not only implementation of infrastructure and some parallel operations, but also description of the problems encountered during the...
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Searching for similar secondary structures in RNA
Vojtek, Daniel ; Hoffmann, Petr (referee) ; Mráz, František (advisor)
In contrast to DNA, the RNA strings fold into complicated secondary structures, which are highly important for their function. Main goal of this work was to create an application, which allows designing a detailed pattern of RNA secondary structure and then finding similar ones in the given set of RNA. The application has also direct access to GenBank database, from which it can download RNA sequences according to the user-defined query. Sequences without secondary structure are folded using a function from Vienna RNA Package. A part of the application is a graphic user interface, which provides comfortable way to design a pattern and allows the browsing found similar secondary structures. The work also presents basic principles of searching of similar RNA secondary structures and its usage in building phylogenetic trees. Description of all used algorithms is present too.
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