Alat za brzo pretraživanje baza proteinskih slijedova

undergraduate thesis

• Title (english): Tool for fast searching of protein sequences in databases
• Author: Ivan Vujević
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Ana Sović Kržić (član povjerenstva)
• Committee member: Juraj Petrović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2014-07-14, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Kod pretrage baza bioloških sljedova postoje dvije vrste algoritama. Jedna vrsta
su deterministički, koji koriste rigorozne algoritme za pronalazak optimalnog rješenja.
Druga vrsta su heuristički algoritmi koji ne pronalaze optimalno rješenje, ali ovi
algoritmi su puno brži od determinističkih algoritama. Potrebno je pronaći kompromis
između brzine i točnosti pretrage.
U ovom radu opisan je heuristički algoritam pretrage. Na početku se za svaki slijed
odredi lista riječi te se tako dobije smanjena baza. Smanjenje cijele baze na listu riječi omogućuje nam bržu pretragu. Algoritam se sastoji od dva koraka. U prvom koraku,
pretragom liste riječi pronalaze se potencijalni kandidati koji se zatim šalju u drugi
korak. U drugom koraku, koristeći jedan od dva algoritma, odabiremo sljedove za
izlaz

Abstract (english)

In database searching are two fundamental types of algorithm. One is deterministic type, which uses a rigorous algorithm to find the best
solution. Another is the heuristic type which don't find optimal solution, but these algorithms are more faster than deterministic type algorithms. We have to find a compromise between speed and accuracy.
In this paper we describe heuristic type of algorithms.At the beginning, for each sequence we have to find word list to get reduced base as a result. Reducing the whole base allows us fastier searching. Algorithm has two steps.
In the first step we find potential candidate and in the
second step we do selection between potential candidate using one of two offered algorithms.

• Keywords: heuristički algoritam; bioinformatika; paralelizacija; biološke baze
• Keywords (english): heuristic algorithm; bioinformatics; parallelization; biological database
• Language: croatian
• URN:NBN: urn:nbn:hr:168:882562
• Study programme: Title: Computing; Study programme type: university; Study level: undergraduate; Academic / professional title: sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva (sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2018-02-06 07:32:58