Sklopovska implementacija postupaka za poravnanje genoma

master's thesis

• Title (english): Hardware implementation of methods for genome alignment
• Author: Marko Polović
• Mentor: Mladen Vučić (mentor)
• Committee member: Mladen Vučić (predsjednik povjerenstva)
• Committee member: Damir Seršić (član povjerenstva)
• Committee member: Mile Šikić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2014-07-17, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Electrical Engineering

Abstract

Količine podataka koje se dobiju sekvenciranjem genoma prevelike su da bi njihovo poravnanje na današnjim računalima trajalo dovoljno kratko. Srećom, mnogi algoritmi za poravnanje se mogu paralelizirati te na taj način ubrzati. U ovom radu razvijen je sustav za poravnavanje koji se temelji na sklopovskoj realizaciji Needleman-Wunschevog algoritma. Sustav je implementiran na programabilnim logičkim poljima familije Virtex-6. Implementirano je 511 paralelnih procesnih elemenata koji povezani u linearno sistoličko polje računaju vrijednost poravnanja. Sustav za poravnanje se s računalom domaćinom povezuje pomoću PCI Express sučelja. Razvijeni sustav pokazuje da sklopovski pristup ima velik potencijal za ubrzavanje postupaka za poravnanje.

Abstract (english)

The amount of data acquired by DNA sequencing is to big for acceptable duration of their alignment on today's computers. Fortunately, many algorithms for alignment can be parallelised thus increasing their execution speed. In this thesis, an alignment system is developed, which is based on hardware realization of the Needleman-Wunsch algorithm. The system is implemented on the field programmable gate arrays of the family Virtex-6. The system is implemented containing 511 processing elements which are connected in a linear systolic array. The alignment system is connected with the host computer via a PCI Express interface. The developed system indicates that hardware approach has a serious potential for the acceleration of alignment algorithms.

• Keywords: poravnavanje genoma; Needleman-Wunsch; programabilna logička polja; FPGA; sustav na čipu; SoC
• Keywords (english): genome alignment; Needleman-Wunsch; field programmable gate arrays; FPGA; system on chip; SoC
• Language: croatian
• URN:NBN: urn:nbn:hr:168:808503
• Study programme: Title: Electrical Engineering and Information Technology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka elektrotehnike i informacijske tehnologije (magistar/magistra inženjer/inženjerka elektrotehnike i informacijske tehnologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2018-02-06 11:21:55