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undergraduate thesis
Pronalaženje varijanti gena iz podataka dobivenih sekvenciranjem
Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing, 2019. urn:nbn:hr:168:510345
Kosier, Sanja
University of Zagreb
Faculty of Electrical Engineering and Computing

Institutional repository: FER Repository

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Kosier, S. (2019). Pronalaženje varijanti gena iz podataka dobivenih sekvenciranjem (Undergraduate thesis). Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing. Retrieved from https://urn.nsk.hr/urn:nbn:hr:168:510345

Kosier, Sanja. "Pronalaženje varijanti gena iz podataka dobivenih sekvenciranjem." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2019. https://urn.nsk.hr/urn:nbn:hr:168:510345

Kosier, Sanja. "Pronalaženje varijanti gena iz podataka dobivenih sekvenciranjem." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2019. https://urn.nsk.hr/urn:nbn:hr:168:510345

Kosier, S. (2019). 'Pronalaženje varijanti gena iz podataka dobivenih sekvenciranjem', Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, accessed 02 September 2024, https://urn.nsk.hr/urn:nbn:hr:168:510345

Kosier S. Pronalaženje varijanti gena iz podataka dobivenih sekvenciranjem [Undergraduate thesis]. Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing; 2019 [cited 2024 September 02] Available at: https://urn.nsk.hr/urn:nbn:hr:168:510345

S. Kosier, "Pronalaženje varijanti gena iz podataka dobivenih sekvenciranjem", Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, 2019. Available at: https://urn.nsk.hr/urn:nbn:hr:168:510345

Metadata
TitlePronalaženje varijanti gena iz podataka dobivenih sekvenciranjem
Title (english)Discovering Gene Variants From Sequencing Data
AuthorSanja Kosier
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
Aleli predstavljaju dva alternativna gena koja određuju istu osobinu. Pronalazak alela iz višestrukih očitanja gena nije trivijalan. Događa se da su određeni aleli u uzorcima podzastupljeni te je teško programskim rješenjima detektirati njihovo pojavljivanje. Cilj ovog rada bio je implementirati metode za pronalazak varijanti gena iz uzoraka dobivenih sekvenciranjem. Problem je riješen korištenjem programskih jezika C++ i Python, alata SPOA i Bioparser te algoritmima za poravnanje sekvenci. Razvijene metode čitaju uzorke iz FASTQ datoteka, koriste višestruko poravnanje sekvenci te vrše grupiranje sličnih očitanja u klastere. Nakon toga, odabiru se najveći klasteri na temelju broja očitanja u njima i računa se konsenzusna sekvenca koja naposljetku predstavlja pronađeni alel. U radu su se koristila očitanja MHC gena divokoza.
Abstract (english)
Alleles represent two alternative genes that determine the same feature of an organism. Finding alleles from multiple readings is not trivial. It is possible that certain alleles in the samples are underrepresented and it is difficult to detect their appearance using software solutions. The aim of this paper was to implement methods for finding gene variants from sequencing data. The problem was solved using C++ and Python programming languages, SPOA and Bioparser tools as well as algorithms for pairwise alignment. Developed methods read samples from FASTQ files, use multiple sequence alignment and perform clustering. Furthermore, the largest clusters are selected based on the number of readings in the clusters and a consensus sequence is generated. A consensus sequence represents a found allele. In this paper the MHC gene samples of chaimos were used.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:168:510345
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 19:14:12