Konstrukcija baze podataka za modularne poliketide i neribosomske peptide

master's thesis

• Title (english): Construction of a database for modular polyketides and non-ribosomal peptides
• Author: Antonio Starčević
• Mentor: Daslav Hranueli (mentor)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Section for Bioinformatics); Zagreb
• Defense date and country: 2004-12-14, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Poliketidi i neribosomski peptidi dvije su najveće skupine mikrobnih sekundarnih metabolita, od kojih mnogi imaju biološki aktivna svojstva. Njihov biosintetski put započinje uzastopnom kondenzacijom jednostavnih građevnih jedinica, te dovodi do izgradnje ugljikovih, tj. peptidnih, lanaca određenih dužina katalitičkim djelovanjem ponavljajućih ili modularnih poliketid sintaza (PKS) i sintaza neribosomskih polipeptida (NRPS). Do sada je kloniran i sekvenciran vrlo velik broj modularnih PKS, NRPS i miješanih modularnih PKS-NRPS sustava. Sekvenciranje svih tih genskih nakupina ukazuje na mogućnost modeliranja procesa rekombinacije između modularnih sintaza pomoću računalnog programa. U konačnici, taj računalni program pruža mogućnost predviđanja kemijskih struktura novonastalih supstancija. Za potrebe tog programa, u ovom je diplomskom radu izrađena baza podataka poznatih poliketida i neribosomskih peptida. Biološki su podaci pohranjeni u relacijskoj bazi podataka MySQL, za čije je upravljanje upotrijebljen računalni jezik SQL. Bazu podataka podržavat će operacijski sustav Linux. Relacijska baza bioloških podataka sadržava: sekvencije DNA i proteina genskih nakupina, gena, modula i domena; kemijske strukture konačnih produkata; metaboličke putove biosinteze i pripadajuću znanstvenu literaturu.

Abstract (english)

Polyketides and non-ribosomal peptides are two largest groups of microbial secondary metabolites. They are synthesised by a series of cycles in which new residues are added to the growing chain of the molecule by iterative or modular polyketide synthase (PKS) or non-ribosomal peptide synthase (NRPS). Up till now, a large number of modular PKS, NRPS or mixed PKS-NRPS systems has been cloned and sequenced. Sequencing of these gene clusters revealed the possibility of modelling the recombination process between modular synthases by a computer program. At the end, such a program allows the prediction of chemical structure of novel compounds. In this diploma work, the biological database of known polyketides and non-ribosomal peptides has been constructed in order to assist the developed computer program. Biological data are stored in relational database MySQL using Sequence Query Language. The database is supported by the Linux operating system. Relational biological database contains: DNA and protein sequences of gene clusters, genes, modules and domains; chemical structures of final products; metabolic biosynthetic pathways and accompanying scientific literature.

• Keywords: računalni operativni sustav Linux; baza podataka MySQL; računalni jezik SQL; neribosomski peptidi; poliketidi
• Keywords (english): Linux operating system; MySQL database; Structured Query Language; non-ribosomal peptides; polyketides
• Language: croatian
• URN:NBN: urn:nbn:hr:159:273017
• Study programme: Title: Biotechnology; specializations in: Biochemical-Microbiology; Course: Biochemical-Microbiology; Study programme type: university; Study level: graduate; Academic / professional title: diplomirani inženjer biotehnologije; smjer biokemijsko-mikrobiološki (diplomirani inženjer biotehnologije; smjer biokemijsko-mikrobiološki)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2017-09-12 13:08:27