Pojednostavljenje grafa preklapanja

master's thesis

• Title (english): Simplification of the overlap graph
• Author: Bruno Rahle
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Mladen Vučić (član povjerenstva)
• Committee member: Damir Seršić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2014-07-07, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

U današnje doba, postoji mnogo različitih metoda sekvenciranja DNK koje se i dalje razvijaju. U ovome radu, prikazujemo kako efikasno odvojiti nepotrebna očitanja i preklapanja iz skupa očitanja i preklapanja koje dobijemo u procesu sekvenciranja DNK. Prikazujemo algoritme za micanje sadržanih očitanja, tranzitivnih bridova, spajanje jedinstvenih spojki i stvaranje grafa niza znakova. Napravljena je implementacija u C++-u i rezultati testiranja su prikazani u ovome radu.

Abstract (english)

Today, a lot of different DNA assembly methods exist and are being actively developed. In this thesis, we show how to efficiently prune unnecessary reads and overlaps from those supplied to us in the process of DNA assembly. We show algorithms for removing contained reads, transitive edges, collapsing unique joins and creating a string graph. A C++ implementation has also been provided and tested, with results presented in this work.

• Keywords: Layout; slaganje DN; Graf nizova znakova; C++
• Keywords (english): Layout; DNA assembly; String graph; C++
• Language: english
• URN:NBN: urn:nbn:hr:168:651874
• Study programme: Title: Computing; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka računarstva (magistar/magistra inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2018-02-06 11:31:03