Alat za poravnanje dugačkih očitanja

undergraduate thesis

• Title (english): Long read aligner
• Author: Marko Ratković
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Andrej Novak (član povjerenstva)
• Committee member: Krešimir Križanović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2015-07-13, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Poravnavanje bioloških sljedova predstavlja jedan od najstarijih i najviše istraživanih problema u bioinformatici. Cilj je identificirati slične regije koje mogu predstavljati funkcionalnu, strukturalnu ili evolucijsku vezu između dvaju organizama.
Neprekidnim razvojem tehnologije napreduju i uređaji za sekvenciranje te su moguća sve duža očitanja. Javlja se potreba za razvojem alata koji će moći poravnati takva dugačka očitanja koja potencijalno mogu imati i visok postotak greške.
U ovom... More radu je predloženo jednostavno rješenje koje problem svodi na problem izdvajanja iz ulaznog slijeda kandidatnih regija korištenjem vrijednosti LCSk++ dvaju podnizova. U radu je dat algoritam, implementacijski detalji razvijenog alate te usporedba s postojećim alatima. Less

Abstract (english)

Sequence allimgent is one of the first and most researched problems in bioinformatics. It is used to identify the regions of similarity that may indicate functional, structural or evolutionary relationship between two organisms
With the advancement of technology, sequencing machines are constantly improving and they are producing longer and longer reads. Need for new aligners that are able to work with those long error-prone exists.
This Thesis presents a simple tool that solves the... More problem of aligning reads by selecting potential regions in a sequence that have higher similarity score. LCSk++ measure between two subsequences is used as similarity score. Described algorithm and implementation details are presented in this Thesis as well as comparison with existing aligners. Less

• Keywords: bioinformatika; poravnanje; dugacka očitanja; LCSk++; sufiksno polje
• Keywords (english): bioinformatics; sequence aligment; long error-prone reads; LCSk++; suffix array
• Language: croatian
• URN:NBN: urn:nbn:hr:168:586716
• 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 11:33:17