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dc.contributor.advisorGutell, Robinen
dc.creatorDoshi, Kishore John, 1974-en
dc.date.accessioned2008-08-28T23:49:59Zen
dc.date.available2008-08-28T23:49:59Zen
dc.date.issued2007en
dc.identifier.urihttp://hdl.handle.net/2152/3471en
dc.description.abstractThe ability of certain RNAs to fold into complicated secondary and tertiary structures provides them with the ability to perform a variety of functions in the cell. Since the secondary and tertiary structures formed by certain RNAs in the cell are central to understanding how they function, one of the most active areas of research has been how to accurately and reliably predict RNA secondary structure from sequence; better known as the RNA Folding Problem. This dissertation examines two fundamental areas of research in RNA structure prediction, free energy minimization and comparative analysis. The most popular RNA secondary structure prediction program, Mfold 3.1 predicts RNA secondary structure via free energy minimization using experimentally determined energy parameters. I present an evaluation of the accuracy of Mfold 3.1 using the largest set of phylogenetically diverse, comparatively predicted RNA secondary structures available. This evaluation will show that despite significant revisions to the energy parameters, the prediction accuracy of Mfold 3.1 is not significantly improved when compared to previous versions. In contrast, RNA comparative analysis has repeatedly demonstrated the ability to accurately and reliably predict RNA secondary structure. The downside is that RNA comparative analysis frequently requires an expert systems methodology which is predominately manual in nature. As a result, RNA comparative analysis is not capable of scaling adequately to be useful in the genomic era. Therefore, I developed the Comparative Analysis Toolkit (CAT) which is intended to be the fundamental component of a vertically integrated software infrastructure to facilitate high-throughput RNA comparative analysis using an expert systems methodology.en
dc.format.mediumelectronicen
dc.language.isoengen
dc.rightsCopyright © is held by the author. Presentation of this material on the Libraries' web site by University Libraries, The University of Texas at Austin was made possible under a limited license grant from the author who has retained all copyrights in the works.en
dc.subject.lcshRNA--Analysis--Computer programsen
dc.subject.lcshNucleotide sequence--Computer programs--Evaluationen
dc.titleRNA secondary structure prediction and an expert systems methodology for RNA comparative analysis in the genomic eraen
dc.description.departmentInstitute for Cellular and Molecular Biologyen
dc.identifier.oclc182575748en
dc.type.genreThesisen
thesis.degree.departmentCellular and Molecular Biology, Institute foren
thesis.degree.disciplineCell and Molecular Biologyen
thesis.degree.grantorThe University of Texas at Austinen
thesis.degree.levelDoctoralen
thesis.degree.nameDoctor of Philosophyen


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