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Analysis of Genomic Data with the Assistance of Algorithm BLAST
Křížová, Martina ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This Bachelor Thesis describes analysis of genomic data with assistance of algorithm BLAST. In theoretic part, it describes genomes, their importance and structure. In this thesis, you can find a description of algorithm BLAST, Smith-Waterman and Needleman-Wunsch and with algorithm BLAST connected Karlin-Altschul statistics. This thesis is discussing types of databases such as spatial, deductive and relational which store genomic data. Second part is concerned with design and implementation of application which use mentioned algorithm and database Oracle 10g R2. Testing and confrontation output of algorithm is also a part of this work.
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Determination genetics differencies using alignment signal of biological sequences DNA
Trněný, Ondřej ; Provazník, Ivo (referee) ; Valla, Martin (advisor)
Biological sequences are constantly evolving so there are mutations, deletions and inserts. Because of need to classify these sequences and determine degree of their similarity have been developed aligment methods. For example Dot matrix or algorithms like Needleman-Wunsch and Smith-Waterman used for global and local alignment. These methods can be considered as conservative and are limited because it is assumed that although there have been changes during evolution they still preserve small distance between similar regions. Therefore number of methods have been proposed to eliminate these limitations by comparing sequences without alignment. These methods for example Words in sequences, Euklidean distance or Universal sequence maps are designed to eliminate limitations of alignment using methods.
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Application for Alignment of DNA Parts
Kašpárek, Tomáš ; Žák, Jakub (referee) ; Rozman, Jaroslav (advisor)
This thesis deals with DNA sequences alignment methods with focus on execution speed of given task and its optimality. The outcome of this thesis results in multiple programs, which presents DNA alignment algorithms and their versions programmed with OpenCL libraries, which are optimized on calculation rate. Text of this thesis apprises reader with DNA alignment problematic and its importance in biology. Further, algorithms for DNA alignment and options of their speed-up using libraries like CUDA or OpenCL are presented.
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Approximate String Matching Algorithm Implementation in FPGA
Pařenica, Martin ; Martínek, Tomáš (referee) ; Fučík, Otto (advisor)
This paper describes sequence alignment algorithms of nucleotide sequences. There are described pairwise alignment algorithms using database search or dynamic programming. Then in the paper is description of dynamic programming for multiple sequences and algorithm that builds phylogenetic trees. At the end of the first part of the paper is the description of technology FPGA. In the second part that is more practical is described implemntation of the choosen one algorithm. This part includes also examples of some multiple alignments.
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Alignment of DNA Parts
Pejř, Václav ; Burgetová, Ivana (referee) ; Rozman, Jaroslav (advisor)
This thesis deals with finding the possibilities within the sphere of alignment of DNA sequences. Based on these findings, the best solution should be found with regard to the quickness of computation and quality of alignment. Following this I intend to implement and thus create a functioning program that will do the alignment. The thesis starts with introducing issues dealing with biology, DNA and genetics. The introduction is followed by a survey of algorithms that are used for alignment, their evaluation and selection of the most appropriate algorithm for the implementation. The thesis also focuses on the usage of parallel programming by means of OpenCL libraries. The alignment is being done above many sequences at the same time, so that the methods how this process can be done and how to reach the best results are being examined.
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Recegnition of Repeating SMS Patterns
Kočalka, Jakub ; Češka, Milan (referee) ; Holík, Lukáš (advisor)
Vďaka pokroku v rozpoznávaní spamu v e-mailoch a zvyšovaní povedomia používateľov smerujú spameri k menej preskúmaným médiám. Jedným z nich je \emph{short messaging service} (SMS). Táto služba poskytuje užívateľom možnosť reagovať na správy v krátkom čase a v skoro ľubovolnom prostredí. Tieto vlastnosti sú atraktívne aj pre legitímne podniky, ktoré potrebujú svojim klinetom zasielať krátke hromadné správy. Aj keď sú tieto správy z pohladu koncového užívateľa vyžiadané, pre poskytovateľa služieb SMS môžu predstavovať stratu, pretože tieto podniky často zneužívajú neobmedzené SMS plány určené pre bežných zákazníkov, aby sa vyhli plateniu za pre nich určené, ale drahšie produkty. Je preto žiaduce vedieť rozpoznať nevyžiadané aj vyžiadané hromadné správy. Hromadné správy sa zvyčajne generujú zo šablóny. Cieľom tejto práce je navrhnúť zhlukovací algoritmus ktorý správy analyzuje ako sekvencie lexikálnych jednotiek (slov), a vyhodnotiť jeho efektivitu v porovnaní s \emph{locality sensitivity hashing} metódou ktorá správy analyzuje ako reťazce symbolov. Práca vyhodnocuje vhodnosť algoritmu Smith-Waterman pre túto úlohu. Práca popisuje, prečo je Smith-Waterman (a ďalšie lokálne zarovnávania) nevhodný, a ako je možné ho nahradiť algoritmom Needleman-Wunsch (globálnym zarovnávaním), aby sa dosiahli oveľa lepšie výsledky. Výsledný algoritmus dokáže uspokojivo zhlukovať skutočné správy do kampaní a funguje dobre aj v situáciách, kde \emph{locality sensitivity hashing} kampane fragmentuje.
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Hardware Acceleration of Algorithms for Approximate String Matching
Nosek, Ondřej ; Kořenek, Jan (referee) ; Martínek, Tomáš (advisor)
Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.
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Recegnition of Repeating SMS Patterns
Kočalka, Jakub ; Češka, Milan (referee) ; Holík, Lukáš (advisor)
Vďaka pokroku v rozpoznávaní spamu v e-mailoch a zvyšovaní povedomia používateľov smerujú spameri k menej preskúmaným médiám. Jedným z nich je \emph{short messaging service} (SMS). Táto služba poskytuje užívateľom možnosť reagovať na správy v krátkom čase a v skoro ľubovolnom prostredí. Tieto vlastnosti sú atraktívne aj pre legitímne podniky, ktoré potrebujú svojim klinetom zasielať krátke hromadné správy. Aj keď sú tieto správy z pohladu koncového užívateľa vyžiadané, pre poskytovateľa služieb SMS môžu predstavovať stratu, pretože tieto podniky často zneužívajú neobmedzené SMS plány určené pre bežných zákazníkov, aby sa vyhli plateniu za pre nich určené, ale drahšie produkty. Je preto žiaduce vedieť rozpoznať nevyžiadané aj vyžiadané hromadné správy. Hromadné správy sa zvyčajne generujú zo šablóny. Cieľom tejto práce je navrhnúť zhlukovací algoritmus ktorý správy analyzuje ako sekvencie lexikálnych jednotiek (slov), a vyhodnotiť jeho efektivitu v porovnaní s \emph{locality sensitivity hashing} metódou ktorá správy analyzuje ako reťazce symbolov. Práca vyhodnocuje vhodnosť algoritmu Smith-Waterman pre túto úlohu. Práca popisuje, prečo je Smith-Waterman (a ďalšie lokálne zarovnávania) nevhodný, a ako je možné ho nahradiť algoritmom Needleman-Wunsch (globálnym zarovnávaním), aby sa dosiahli oveľa lepšie výsledky. Výsledný algoritmus dokáže uspokojivo zhlukovať skutočné správy do kampaní a funguje dobre aj v situáciách, kde \emph{locality sensitivity hashing} kampane fragmentuje.
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Analysis of Genomic Data with the Assistance of Algorithm BLAST
Křížová, Martina ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This Bachelor Thesis describes analysis of genomic data with assistance of algorithm BLAST. In theoretic part, it describes genomes, their importance and structure. In this thesis, you can find a description of algorithm BLAST, Smith-Waterman and Needleman-Wunsch and with algorithm BLAST connected Karlin-Altschul statistics. This thesis is discussing types of databases such as spatial, deductive and relational which store genomic data. Second part is concerned with design and implementation of application which use mentioned algorithm and database Oracle 10g R2. Testing and confrontation output of algorithm is also a part of this work.
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Determination genetics differencies using alignment signal of biological sequences DNA
Trněný, Ondřej ; Provazník, Ivo (referee) ; Valla, Martin (advisor)
Biological sequences are constantly evolving so there are mutations, deletions and inserts. Because of need to classify these sequences and determine degree of their similarity have been developed aligment methods. For example Dot matrix or algorithms like Needleman-Wunsch and Smith-Waterman used for global and local alignment. These methods can be considered as conservative and are limited because it is assumed that although there have been changes during evolution they still preserve small distance between similar regions. Therefore number of methods have been proposed to eliminate these limitations by comparing sequences without alignment. These methods for example Words in sequences, Euklidean distance or Universal sequence maps are designed to eliminate limitations of alignment using methods.
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