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undergraduate thesis
Korištenje referentne baze za predviđanje plazmida
Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing, 2019. urn:nbn:hr:168:459130
Deur, Sanja
University of Zagreb
Faculty of Electrical Engineering and Computing

Institutional repository: FER Repository

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Deur, S. (2019). Korištenje referentne baze za predviđanje plazmida (Undergraduate thesis). Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing. Retrieved from https://urn.nsk.hr/urn:nbn:hr:168:459130

Deur, Sanja. "Korištenje referentne baze za predviđanje plazmida." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2019. https://urn.nsk.hr/urn:nbn:hr:168:459130

Deur, Sanja. "Korištenje referentne baze za predviđanje plazmida." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2019. https://urn.nsk.hr/urn:nbn:hr:168:459130

Deur, S. (2019). 'Korištenje referentne baze za predviđanje plazmida', Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, accessed 16 June 2024, https://urn.nsk.hr/urn:nbn:hr:168:459130

Deur S. Korištenje referentne baze za predviđanje plazmida [Undergraduate thesis]. Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing; 2019 [cited 2024 June 16] Available at: https://urn.nsk.hr/urn:nbn:hr:168:459130

S. Deur, "Korištenje referentne baze za predviđanje plazmida", Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, 2019. Available at: https://urn.nsk.hr/urn:nbn:hr:168:459130

Metadata
TitleKorištenje referentne baze za predviđanje plazmida
Title (english)Using Reference Database for Plasmid Prediction
AuthorSanja Deur
MentorMile Šikić (mentor)
Committee memberMile Šikić (predsjednik povjerenstva)
Committee memberKrešimir Križanović (član povjerenstva)
Committee memberJosip Marić (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Electrical Engineering and Computing
Zagreb
Defense date and country2019-07-12, 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 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.
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 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.
Keywords
Keywords (english)
Languageenglish
URN:NBNurn:nbn:hr:168:459130
Study programmeTitle: 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 resourceText
File originBorn digital
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Created on2020-01-07 17:34:43