Thesis Details

Implementace algoritmu pro hledání podobností DNA řetězců v FPGA

Master's Thesis Student: Pařenica Martin Academic Year: 2006/2007 Supervisor: Fučík Otto, doc. Dr. Ing.
English title
Approximate String Matching Algorithm Implementation in FPGA
Language
Czech
Abstract

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 isdescription 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 secondpart that is more practical is described implemntation of the choosen one algorithm. This part includes also examples of some multiple alignments.

Keywords

DNA, pairwise alignment, database search, BLAST, FASTA, Needleman-Wunsch, Smith-Waterman, multiple alignment, dynamic programming, CLUSTAL, phylogenetic tree, FPGA.

Department
Degree Programme
Information Technology, Field of Study Computer Systems and Networks
Files
Status
defended, grade B
Date
19 June 2007
Reviewer
Committee
Dvořák Václav, prof. Ing., DrSc. (DCSY FIT BUT), předseda
Janoušek Vladimír, doc. Ing., Ph.D. (DITS FIT BUT), člen
Kotásek Zdeněk, doc. Ing., CSc. (DCSY FIT BUT), člen
Krejčíček Jaromír, prof. Ing., CSc. (UNOB), člen
Křena Bohuslav, Ing., Ph.D. (DITS FIT BUT), člen
Matoušek Petr, doc. Ing., Ph.D., M.A. (DIFS FIT BUT), člen
Citation
PAŘENICA, Martin. Implementace algoritmu pro hledání podobností DNA řetězců v FPGA. Brno, 2007. Master's Thesis. Brno University of Technology, Faculty of Information Technology. 2007-06-19. Supervised by Fučík Otto. Available from: https://www.fit.vut.cz/study/thesis/4811/
BibTeX
@mastersthesis{FITMT4811,
    author = "Martin Pa\v{r}enica",
    type = "Master's thesis",
    title = "Implementace algoritmu pro hled\'{a}n\'{i} podobnost\'{i} DNA \v{r}et\v{e}zc\r{u} v FPGA",
    school = "Brno University of Technology, Faculty of Information Technology",
    year = 2007,
    location = "Brno, CZ",
    language = "czech",
    url = "https://www.fit.vut.cz/study/thesis/4811/"
}
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