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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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Effects of hyperparameters in multiple sequence alignment for Align-RUDDER using Clustal
SAMWALD, Christian
Delayed rewards are detrimental to the learning of reinforcement learning agents.One approach to this problem is the usage of return decomposition and rewardredistribution. It was realised in the Align-RUDDER algorithm of Patilet al.[14].Their solution employed the multiple sequence alignment algorithm Clustal W. Iintegrated the sequence alignment Tool Clustal, Clustal W's successor, intoAlign RUDDER to increase efficiency. During the testing process, the usage ofClustal's EPA function and the effects of different sample sizes played a centralrole. The data set that was used came from the MineRL data set [6].
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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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