Show simple item record

dc.contributor.authorKong, Hoi Yee
dc.date.accessioned2016-01-08T01:49:35Z
dc.date.available2016-01-08T01:49:35Z
dc.date.issued2015
dc.identifier.urihttps://hdl.handle.net/10182/6777
dc.description.abstractRecent advances in high-throughput technologies and the corresponding growth of the bioinformatics databases, a lot of bioinformatics tools have been constantly developed and published in journals for data-intensive genetic analysis. However, repoducibility has been one of the biggest challenges in delivering bioinformatics. Virtualisation is one of the most commonly used solutions by creating virtualised and isolated environments for running different bioinformatics tools. Containerisation, however, is a more recent, promising, scalable and reproducible approach for delivering bioinformatics. It allows running bioinformatics tools on preconfigured containerised environments, which is lightweight and can be easily updated and shared between researchers. This dissertation has evaluated a bioinformatics toolkit previously developed for genetic marker design in preconfigured containers. The objectives for this dissertation were (1) to improve marker design software to correctly handle melt prediction of amplicons with multiple SNPs, (2) using containerised environments to design and screen PCR assay to (a) validate candidate SNPs detected by GBS of barley H. bulbosum introgression line, (b) validate QTL markers of wheat identified by GWAS on chromosome 1A, and (c) convert SNPs from 90K SNP chip for the bread wheat A genome to HRM markers.en
dc.language.isoenen
dc.publisherLincoln Universityen
dc.subjectbioinformaticsen
dc.subjecthigh throughput sequencing analysisen
dc.subjectreproducibilityen
dc.subjectvirtualisationen
dc.subjectsingle nucleotide polymorphismen
dc.subjectmarker assisted selectionen
dc.subjectcleaved amplified polymorphic sequence (CAPS)en
dc.subjecthigh resolution meltingen
dc.subjectwheaten
dc.subjectcontainerisationen
dc.titleDevelopment of a SNP validation toolset for wheaten
dc.typeDissertationen
thesis.degree.nameBachelor of Science (Honours)en
lu.thesis.supervisorWinefield, Chris
lu.contributor.unitDepartment of Wine, Food and Molecular Biosciencesen
dc.subject.anzsrc080204 Mathematical Softwareen
dc.subject.anzsrc060705 Plant Physiologyen
dc.subject.anzsrc070103 Agricultural Production Systems Simulationen


Files in this item

Default Thumbnail

This item appears in the following Collection(s)

Show simple item record