Naslov
Memorijski učinkovita pohrana genoma iste vrste
(Memory-Efficient Storage of Multiple Genomes of the Same Species)

Autori
Kodžoman, Vinko

Vrsta, podvrsta i kategorija rada
Ocjenski radovi, diplomski rad, preddiplomski

Fakultet
Fakultet elektrotehnike i računarstva

Mjesto
Zagreb

Datum
02.07

Godina
2015

Stranica
43

Mentor
Domazet-Lošo, Mirjana

Ključne riječi
Referentni genom; Indeks; Burrows-Wheelerova transformacija; Sufiksno polje; Pretraživanje uzoraka
(Reference genome; Index; Burrows-Wheeler Transform; Suffix array; Pattern searching)

Sažetak
In this thesis I address the problem of memory-efficient representation of a collection of genomes and their indexing. I have developed a reference genome index based on a Burrows-Wheeler transform aligner called BWBBLE. To increase its flexibility, I have added custom code tables and created an input/output engine that enables creation of a reference genome from a genome population. The index is written in the C++ programming language and compared to BWA – a software package for mapping sequences against a large reference genome. The reference genome index is not competitive to the BWA performance-wise but it allows more flexibility, allowing the user to create a reference genome and input their own code tables.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Računarstvo

POVEZANOST RADA