Izrada računalnih alata za analizu podataka o crijevnom mikrobiomu

master's thesis

• Title (english): Development of computer tools for gut microbiome data analysis
• Author: Katarina Prskalo
• Mentor: Janko Diminić (mentor)
• Committee member: Jurica Žučko (predsjednik povjerenstva); : 74534184539
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Section for Bioinformatics); Zagreb
• Defense date and country: 2020-07-13, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Zbog napretka tehnologije sekvenciranja došlo je do eksponencijalnog rasta broja mikrobnih sekvenci u bazama podataka, a metagenomskom analizom dobivaju se kompleksni podaci o taksonomskim profilima i metaboličkim funkcijama. Obrada podataka je sve veći izazov stoga postoji potreba za razvojem računalnih alata koji će olakšati i skratiti vrijeme utrošeno na analize koje je moguće automatizirati. Programski alat razvijen u sklopu ovog diplomskog rada omogućuje grafički prikaz i statističku obradu podataka dobivenih metagenomskom analizom pomoću MetaPhlAn alata. Programski alat napisan je programskim jezikom Python te sadrži pet programa koji vrše obradu podataka i jedan testni program u kojem je moguće testirati funkcionalnosti ostalih. Programi uzimaju različite parametre s kojima je moguće mijenjati prikaz rezultata čime se dobiva na varijaciji u prikazu čime se olakšava interpretacija podataka.

Abstract (english)

Advancements in sequencing technology gave way to exponential growth in number of microbial sequences in databases, whereas metagenomic analysis results are complex data that include taxonomic profiles and metabolic functions. Data processing is gradually becoming a bigger challenge, therefore development of computer tools is required to facilitate and reduce time needed for analyses that are possible to automate. The software tool developed as a part of this master thesis enables graphical display and statistical analysis of data gained through metagenomic analysis with the MetaPhlAn tool. The software tool is coded with Python programing language and contains five programs that process data and one testing program with which is possible to test functions of others. Programs take different parameters which permit changes in showing results that enables variation in displaying which facilitates data interpretation.

• Keywords: crijevni mikrobiom; metagenomika; taksonomski profil; bioraznolikost
• Keywords (english): gut microbiome; metagenomics; taxonomic profile; biodiversity
• Language: croatian
• URN:NBN: urn:nbn:hr:159:579511
• Study programme: Title: Molecular Biotechnology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka molekularne biotehnologije (magistar/magistra inženjer/inženjerka molekularne biotehnologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Repository: Repository of the Faculty of Food Technology and Biotechnology
• Created on: 2020-07-13 12:20:19