Korištenje referentne baze za predviđanje plazmida

undergraduate thesis

• Title (english): Using Reference Database for Plasmid Prediction
• Author: Sanja Deur
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Krešimir Križanović (član povjerenstva)
• Committee member: Josip Marić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2019-07-12, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Glavna zadaća ovoga rada jest analiza algoritma zaduženog za predviđanje
plazmida na temelju referentne baze za kratka očitanja, temeljenog na BLAST-u, te
razvoj novog algoritma temeljenog na algoritmu minimap2. Unatoč tome što ima
kraće vrijeme izvođenja, algoritam razvijen u ovom radu pokazuje slabije rezultate
klasifikacije, nego postojeći BLAST algoritam, stoga su potrebna buduća
poboljšanja. Klasifikacija se provodi i na poznatim i na nepoznatim plazmidima i
kromosomima, koji su... More podijeljeni na podnizove duljine k. Nadalje, unakrsna
validacija provodi se za tri najučestalije i medicinski najbitnije vrste bakterija u bazi,
sljedećih naziva: Escherichia Coli, Klebsiella Pneumoniae i Salmonella enterica.
Izvorni kod dostupan je na: https://github.com/lbcb-edu/BSc-thesis-18-
19/tree/sdeur. Less

Abstract (english)

The main concern of this thesis is analysis of a reference based plasmid prediction
algorithm for short read assemblies based on BLAST, and development of novel
algorithm based on minimap2. Even though it has shorter execution time, thesis’
algorithm demonstrates poorer classification results than existing BLAST algorithm,
so future improvements are needed. Classification is conducted on both known and
unknown plasmids and chromosomes, which are parted in k-length subsequences
in... More order to mimic incomplete assemblies. Furthermore, cross-validation is carried
out for the three most frequent and clinically important bacterial species in database:
Escherichia Coli, Klebsiella Pneumoniae and Salmonella enterica. Source code is
available at: https://github.com/lbcb-edu/BSc-thesis-18-19/tree/sdeur. Less

• Keywords: bakterija; plazmid; kromosom; klasifikacija; unakrsna validacija
• Keywords (english): bacterium; plasmid; chromosome; classification; cross-validation
• Language: english
• URN:NBN: urn:nbn:hr:168:459130
• 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: 2020-01-07 17:34:43