Optimizacija i usporedba algoritama za sravnjivanje kratkih sekvencija prote

master's thesis

• Title (english): Optimization and comparison of algorithms for aligning of short protein sequences
• Author: Ante Tomasović
• Mentor: Antonio Starčević (mentor)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Section for Bioinformatics); Zagreb
• Defense date and country: 2015-07-20, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Razvojem novih metoda sekvencioniranja DNA i proteina, došlo je do naglog porasta broja podataka pohranjenih u javno dostupnim bazama. Glavninu tih podataka čine upravo nukleotidne i aminokiselinske sekvencije. Ključ pretraživanja rastućih baza podataka je u razvoju programa koji mogu brzo pretražiti i usporediti sekvencu upita sa sekvencama iz baze podataka. Najpopularniji takav program je BLAST, kojem se može pristupiti mrežno ili ga se može koristiti lokalno. BLAST kao takav nije dizajniran da pretražuje kratke peptidne sekvence (manje od 20 aminokiselina) ali ga se može koristiti u tu svrhu. Cilj ovog diplomskog rada jest usporedba rezultata pretraživanja kratkih aminokiselinskih sekvencija uz pomoć dva raspoloživa programska alata, riječ je o gore spomenutom BLAST-u i njegovoj alternativi nazvanoj RAPSearch2. U radu se uspoređivala brzina pretraživanja i preciznost pojedinog programa kako bi se ustvrdilo koji je program prikladniji u svrhu pretrage kratkih peptidnih sekvenci iz velikih baza podataka.

Abstract (english)

With the development of new methods for DNA and protein sequencing, there has been a rise in the number and quantity of known DNA and protein sequences. The key for searching through the large databases that contain those sequences is in the development of programs that can quickly compare a query sequence with those contained in a database. The most popular program for such a purpose is BLAST, which can be accessed by internet or it can be installed and accessed locally. The goal of the thesis was to compare the results of the search containing short protein sequences as query and carried out by two bioinformatic tools, namely BLAST and RAPSearch2. The speed of the search and the precision of the results obtained were compared in both cases. The purpose of this work was to find out which program is more suitable for querying short protein sequences against a large database.

• Keywords: BLAST; RAPSearch2; kratke peptidne sekvence; broj pogodaka; brzina pretraživanja
• Keywords (english): BLAST; RAPSearch2; short peptide sequences; number of hits; the speed of the search
• Language: croatian
• URN:NBN: urn:nbn:hr:159:001355
• 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: Access restricted to students and staff of home institution
• Created on: 2017-04-28 12:52:20