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dc.contributor.authorGirilishena, Yaroslava
dc.date.accessioned2017-10-23T17:45:33Z
dc.date.available2017-10-23T17:45:33Z
dc.identifier.urihttp://hdl.handle.net/10464/13070
dc.description.abstractWhile a large number of methods have been developed to detect such types of genome sequence variations as single nucleotide polymorphisms (SNPs) and small indels, comparatively fewer methods have been developed for finding structural variants (SVs) and in particular mobile elements insertions (MEIs). Moreover, almost all these methods can detect only the breakpoints of an occurred SV, sometimes with approximation, and do not provide complete sequences representing the SVs. The main objective of our research is to develop a set of computer algorithms to provide complete genome sequence characterization for insertional structural variants in the human genomes via local de novo sequence assembly or progressive assembly using discordant and concordant read pairs and split-reads. An essential component of our approach involves utilizing all personal genome data available in the public domain vs. the standard way of using one set of personal genome sequences. The developed tool is the first system that provides full sequence characterization of SVs. Overall, the characterization success rate for Alu is 75.03% with the mean of discordant and split-reads higher than 94 reads. For SVA, it is 71.43% with the threshold of 363 reads. And for L1 the values are 77.78% and 355 respectively. The results showed that the SV characterization depends on the allele frequency and is influenced by the repetitiveness of flanking regions. Therefore, addressing these problems is a key to further improvements.en_US
dc.language.isoengen_US
dc.publisherBrock Universityen_US
dc.subjectcomplete sequence characterizationen_US
dc.subjectlocal assemblyen_US
dc.subjectMEI characterizationen_US
dc.subjectmobile element insertionen_US
dc.subjectstructural variationen_US
dc.subjectAluen_US
dc.subjectSVAen_US
dc.subjectL1en_US
dc.subjectsplit-readen_US
dc.subjectdiscordant read pairen_US
dc.titleComplete computational sequence characterization of mobile element variations in the human genome using meta-personal genome dataen_US
dc.typeElectronic Thesis or Dissertationen
dc.degree.nameM.Sc. Computer Scienceen_US
dc.degree.levelMastersen_US
dc.contributor.departmentDepartment of Computer Scienceen_US
dc.degree.disciplineFaculty of Mathematics and Scienceen_US
refterms.dateFOA2021-08-01T01:39:57Z


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