Popunjavanje rupa u djelomično sastavljenom genomu

undergraduate thesis

• Title (english): Gap Filling in a Partially Assembled Genome
• Author: Marija Oreč
• Mentor: Krešimir Križanović (mentor)
• Committee member: Krešimir Križanović (predsjednik povjerenstva)
• Committee member: Filip Bosnić (član povjerenstva)
• Committee member: Josip Marić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2022-06-23, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

U današnje vrijeme, uređaji za postupak sekvenciranja ograničeni su na očitanje manjih dijelova s određenom pogreškom. Pošto ne sekvenciraju cijele genome, jedan od glavnih zadataka u bioinformatici jest sastavljanje cijelog genoma na temelju nastalih očitanja. Razvijeni alati za ovaj problem za velike genome sastavljaju manje dijelove koje nazivamo djelomično sastavljenim fragmentiranim genomima. Potrebno je razviti dodatne alate za poboljšanje takvih djelomično sastavljenih genoma. U ovom radu se sastavljeni genom pokušava dobiti korištenjem algoritma zvanog HERA. Ovaj pristup je temeljen na izgradnji grafa preklapanja te traženju adekvatne staze za konstruiranje cjelovite sekvence. Rezultati razvijenog alata prikazani su nad testnim primjerima.

Abstract (english)

Nowadays, sequencers are limited to reading smaller parts with a certain error. Since they do not sequence the entire genome, one of the main tasks in Bionfortmatics is to assemble whole genomes based on the resulting reads. Developed tools for this problem assemble smaller parts of large genomes that we call partially assembled fragmented genomes. Additional tools need to be developed to improve such partially fragmented genomes. In this paper, a complete genome is attempted to be obtained using an algorithm called HERA. This approach is based on the construction of an overlap graph and finding adequate paths for constructing complete sequences. The results of the developed tool are shown above the test examples.

• Keywords: bioinformatika; sastavljanje; djelomično; genom; HERA
• Keywords (english): bioinformatics; assembly; partially; genome; HERA
• Language: croatian
• URN:NBN: urn:nbn:hr:168:203563
• 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: 2023-01-14 21:20:03