Webová aplikácia pre výber sekvenačných primerov pre amplikónové sekvenovanie 16S rRNA

English title

Web Application for Primer Selection for 16S rRNA Amplicon Sequencing

Language

Czech

Abstract

Main goal of this thesis was an implementation of web application, that can evalutate and recommend primer pairs for 16S rRNA amplicon sequencing, according to users specific needs and by this simplify the procces of primer pair selection. Primer pair evaluation is based on database of primer pairs, which contains data about senzitivity and specifity of each primer pair. Part of the work was also the performance optimization of the primer pair analysis algorithm, that computes senzitivity and specifity data. This optimization helped in an integration of algorithm into the application, which means that users can submit their own primer pair sequences, run analysis and get informations about position of amplified region, sensitivity and specifity.

Keywords

metagenomic, 16S rRNA, amplicon sequencing, PCR, primer, web application

Department

Department of Computer Systems FIT BUT

Degree Programme

Information Technology and Artificial Intelligence, Specialization Bioinformatics and Biocomputing

Files

Status

defended, grade A

Date

21 June 2022

Reviewer

Martínek Tomáš, doc. Ing., Ph.D.

Committee

Sekanina Lukáš, prof. Ing., Ph.D. (DCSY FIT BUT), předseda
Bidlo Michal, doc. Ing., Ph.D. (DCSY FIT BUT), člen
Burgetová Ivana, Ing., Ph.D. (DIFS FIT BUT), člen
Lengál Ondřej, Ing., Ph.D. (DITS FIT BUT), člen
Matoušek Radomil, doc. Ing., Ph.D. (IACS FME BUT), člen
Vašíček Zdeněk, doc. Ing., Ph.D. (DCSY FIT BUT), člen

Citation

JURČA, Jan. Webová aplikácia pre výber sekvenačných primerov pre amplikónové sekvenovanie 16S rRNA. Brno, 2022. Master's Thesis. Brno University of Technology, Faculty of Information Technology. 2022-06-21. Supervised by Smatana Stanislav. Available from: https://www.fit.vut.cz/study/thesis/25131/

BibTeX

@mastersthesis{FITMT25131,
    author = "Jan Jur\v{c}a",
    type = "Master's thesis",
    title = "Webov\'{a} aplik\'{a}cia pre v\'{y}ber sekvena\v{c}n\'{y}ch primerov pre amplik\'{o}nov\'{e} sekvenovanie 16S rRNA",
    school = "Brno University of Technology, Faculty of Information Technology",
    year = 2022,
    location = "Brno, CZ",
    language = "czech",
    url = "https://www.fit.vut.cz/study/thesis/25131/"
}