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dc.contributor.authorWarren, Andrew Scotten_US
dc.date.accessioned2019-01-11T07:00:35Z
dc.date.available2019-01-11T07:00:35Z
dc.date.issued2017-07-19
dc.identifier.othervt_gsexam:11481en_US
dc.identifier.urihttp://hdl.handle.net/10919/86660
dc.description.abstractResearch in comparative microbial genomics has largely been organized around the concept of reference genomes. Reference genomes provide a useful comparative touchstone for closely related organisms. However, they do not necessarily well represent the biological diversity in a group of genomes. As sampling through sequencing becomes both deeper and broader, reference genome based methods become less effective at characterizing groups of organisms. We present an algorithm for creating whole genome multiple sequence comparisons and a model for representing the similarities and differences among sequences as a graph of syntenic gene families called a pan-synteny graph. As the evolutionary distance between organisms increase sequence similarity and homology detection tend to break down. However, similarities in the functional characteristics of certain genes and gene modules may persist or have converged over time. Detecting and defining patterns in these functional similarities, in relation to conserved gene order, is a largely unexplored problem. To create a model for representing the architectural similarity of functional modules, using ontologies and semantic similarity, we present a corpus independent semantic similarity method, and describe a computational framework for using semantic similarity and pan-synteny graphs.en_US
dc.format.mediumETDen_US
dc.publisherVirginia Techen_US
dc.rightsThis item is protected by copyright and/or related rights. Some uses of this item may be deemed fair and permitted by law even without permission from the rights holder(s), or the rights holder(s) may have licensed the work for use under certain conditions. For other uses you need to obtain permission from the rights holder(s).en_US
dc.subjectComputer scienceen_US
dc.subjectBioinformaticsen_US
dc.subjectMicrobiologyen_US
dc.titleMethods for Analysis of Prokaryotic Genome Architectureen_US
dc.typeDissertationen_US
dc.contributor.departmentComputer Scienceen_US
dc.description.degreePh. D.en_US
thesis.degree.namePh. D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen_US
thesis.degree.disciplineComputer Science and Applicationsen_US
dc.contributor.committeechairHeath, Lenwood S.en_US
dc.contributor.committeechairSetubal, Joao Carlosen_US
dc.contributor.committeememberMurali, T M.en_US
dc.contributor.committeememberDickerman, Allan W.en_US
dc.contributor.committeememberFriedberg, Iddoen_US
dc.contributor.committeememberZhang, Liqingen_US


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