Alat za poravnavanje genoma

undergraduate thesis

• Title (english): Whole-genome alignment tool
• Author: Petar Žuljević
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Ana Sović Kržić (član povjerenstva)
• Committee member: Juraj Petrović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2014-09-17, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Poravnanje genoma je jedan od većih problema u bioinformatici koji još uvijek nije efikasno riješen. Iako su poznati egzaktni algoritmi kojima bi se moglo doći do optimalnog rješenja, oni se ipak ne koriste jer bi njihovo izvođenje zahtijevalo previše vremena.

U radu je opisan alat za poravnanje genoma ostvaren kao višedretveni program u programskom jeziku C++. Alat se bazira na pronalasku identičnih podnizova zadanih genoma pomoću sufiksnog polja, a nakon toga na primjeni algoritma Smith-Waterman na područja u kojima nisu pronađeni MUMovi. Konačan rezultat je grafički prikaz koji prikazuje identične, translatirane i reverzno komplementirane regije u zadanim genomima.

Abstract (english)

Genome alignment is one of the major problems in bioinformatics that still have not been effectively resolved. Although exact algorithms which would give optimal solution are known, they are not used because of their long running time.

In this thesis is described tool for genome alignment realized like multithreaded application written in C++. Tool is based on locating identical interval regions in given genomes by using suffix array, and after that by using Smith-Waterman algorithm on regions in which MUMs were not found. Final result is graphical representation of identical, translocated and reverse complemented regions in given genomes.

• Keywords: Poravnanje; genom; sufiksno polje; paralelizacija; heuristika; bioinformatika
• Keywords (english): Alignment; genome; suffix array; parallelization; heuristics; bioinformatics
• Language: croatian
• URN:NBN: urn:nbn:hr:168:394268
• Study programme: Title: Computing; Study programme type: university; Study level: undergraduate; Academic / professional title: sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva (sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2018-02-06 14:38:24