Thesis Details

Akcelerace algoritmů pro porovnání biologických sekvencí s využitím FPGA

Bachelor's Thesis Student: Beck Patrik Academic Year: 2006/2007 Supervisor: Martínek Tomáš, doc. Ing., Ph.D.

English title

Acceleration of Algorithms for Approximate String Matching Using FPGA

Language

Czech

Abstract

This work describes implementation of hardware device for approximate string matching of biological sequences. Matchnig is performed using Smith-Waterman and Needleman-Wunsch algorithms. Device can be used as an accelerator for bioinformatics algorithms onhigher level. This accelerator can be used for human genome analysis, matching proteins against a database, revealing inheritance information. Depending on task character, the acceleration speed up achieves several orders of magniture in comparison with conventionalcomputers.

Keywords

FPGA, approximate string matching

Department

Department of Computer Systems FIT BUT

Degree Programme

Information Technology

Files

Thesis text 927 kB

Status

defended, grade A

Date

12 June 2007

Reviewer

Kořenek Jan, doc. Ing., Ph.D.

Committee

Sekanina Lukáš, prof. Ing., Ph.D. (DCSY FIT BUT), předseda
Černocký Jan, prof. Dr. Ing. (DCGM FIT BUT), člen
Fučík Otto, doc. Dr. Ing. (DCSY FIT BUT), člen
Herout Adam, prof. Ing., Ph.D. (DCGM FIT BUT), člen
Jedlička Petr, Ing., Ph.D. (Mendelu), člen
Peringer Petr, Dr. Ing. (DITS FIT BUT), člen

Citation

BECK, Patrik. Akcelerace algoritmů pro porovnání biologických sekvencí s využitím FPGA. Brno, 2007. Bachelor's Thesis. Brno University of Technology, Faculty of Information Technology. 2007-06-12. Supervised by Martínek Tomáš. Available from: https://www.fit.vut.cz/study/thesis/5106/

BibTeX

@bachelorsthesis{FITBT5106,
    author = "Patrik Beck",
    type = "Bachelor's thesis",
    title = "Akcelerace algoritm\r{u} pro porovn\'{a}n\'{i} biologick\'{y}ch sekvenc\'{i} s vyu\v{z}it\'{i}m 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/5106/"
}

Theses