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dc.contributor.advisorKusalik, Anthony J. (Tony)en_US
dc.contributor.advisorParkin, Isobel A. P.en_US
dc.creatorLewis, Christopher Thomasen_US
dc.date.accessioned2009-05-06T10:05:13Zen_US
dc.date.accessioned2013-01-04T04:30:28Z
dc.date.available2010-05-25T08:00:00Zen_US
dc.date.available2013-01-04T04:30:28Z
dc.date.created2008en_US
dc.date.issued2008en_US
dc.date.submitted2008en_US
dc.identifier.urihttp://hdl.handle.net/10388/etd-05062009-100513en_US
dc.description.abstractIn the post-genomics era, the sheer volume of data is overwhelming without appropriate tools for data integration and analysis. Studying genomic sequences in the context of other related genomic sequences, i.e. comparative genomics, is a powerful technique enabling the identification of functionally interesting sequence regions based on the principal that similar sequences tend to be either homologous or provide similar functionality. Costs associated with full genome sequencing make it infeasible to sequence every genome of interest. Consequently, simple, smaller genomes are used as model organisms for more complex organisms, for instance, Mouse/Human. An annotated model organism provides a source of annotation for transcribed sequences and other gene regions of the more complex organism based on sequence homology. For example, the gene annotations from the model organism aid interpretation of expression studies in more complex organisms. To assist with comparative genomics research in the Arabidopsis/Brassica (Thale-cress/Canola) model-crop pair, a web-based, graphical genome browser (BioViz) was developed to display short Brassica genomic sequences in the context of the Arabidopsis model organism genome. This involved the development of graphical representations to integrate data from multiple sources and tools, and a novel user interface to provide the user with a more interactive web-based browsing experience. While BioViz was developed for the Arabidopsis/Brassica comparative genomics context, it could be applied to comparative browsing relative to other reference genomes. BioViz proved to be an valuable research support tool for Brassica / Arabidopsis comparative genomics. It provided convenient access to the underlying Arabidopsis annotation, allowed the user to view specific EST sequences in the context of the Arabidopsis genome and other related EST sequences. In addition, the limits to which the project pushed the SVG specification proved influential in the SVG community. The work done for BioViz inspired the definition of an opensource project to define standards for SVG based web applications and a standard framework for SVG based widget sets.en_US
dc.language.isoen_USen_US
dc.subjectBioinformaticsen_US
dc.subjectComparative Genomicsen_US
dc.subjectVisualizationen_US
dc.subjectScalable Vector Graphics (SVG)en_US
dc.titleRepresenting short sequences in the context of a model organism genomeen_US
thesis.degree.departmentComputer Scienceen_US
thesis.degree.disciplineComputer Scienceen_US
thesis.degree.grantorUniversity of Saskatchewanen_US
thesis.degree.levelMastersen_US
thesis.degree.nameMaster of Science (M.Sc.)en_US
dc.type.materialtexten_US
dc.type.genreThesisen_US
dc.contributor.committeeMemberMcQuillan, Ianen_US
dc.contributor.committeeMemberLu, Paulen_US
dc.contributor.committeeMemberKeil, J. Marken_US
dc.contributor.committeeMemberCovello, Patrick S.en_US
dc.contributor.committeeMemberAngel, Joseph F.en_US


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