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dc.contributor.authorMcCarthy, Eugene Michael
dc.date.accessioned2014-03-03T20:25:56Z
dc.date.available2014-03-03T20:25:56Z
dc.date.issued2003-05
dc.identifier.othermccarthy_eugene_m_200305_phd
dc.identifier.urihttp://purl.galileo.usg.edu/uga_etd/mccarthy_eugene_m_200305_phd
dc.identifier.urihttp://hdl.handle.net/10724/20856
dc.description.abstractThe research presented in this dissertation consists of three parts: 1) a description of the design and function of a novel data-mining program, LTR_STRUC; 2) a survey of LTR retrotransposons in the rice genome; 3) a survey of LTR retrotransposons in the mouse genome. The algorithm used by LTR_STRUC differs at a fundamental conceptual level from that employed in BLAST-type, query-based programs and thus provides an alternative, complementary method of identifying LTR retrotransposons in necleotide sequence data. We combined LTR_STRUC and conventional techniques to thoroughly search of the rice and mouse genomes for LTR retrotransposons. In rice, we found 59 families (37 copia-like, 20 gypsy-like, 2 non-autonomous). In mouse, we found 20 (all gypsy-like). In both species, we were able to more than double the number of recognized LTR retrotransposon families, a testament to the efficacy of LTR_STRUC-supported retrotransposon surveys.
dc.languageeng
dc.publisheruga
dc.rightspublic
dc.subjectOryza sativa
dc.subjectMus musculus
dc.subjectcopia
dc.subjectgypsy
dc.subjectTransposable element
dc.subjectRetrotransposon
dc.subjectLTR
dc.subjectData-miner
dc.subjectSearch algorithm
dc.titleLTR_STRUC, a novel data-mining tool, and its application to the rice and mouse genomes
dc.typeDissertation
dc.description.degreePhD
dc.description.departmentGenetics
dc.description.majorGenetics
dc.description.advisorJohn F. McDonald
dc.description.committeeJohn F. McDonald
dc.description.committeeEthan W. Taylor
dc.description.committeeEileen Kraemer
dc.description.committeeDaniel Promislow
dc.description.committeeJohn Avise


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