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dc.contributor.authorLiu, Renyi
dc.date.accessioned2014-03-03T20:01:44Z
dc.date.available2014-03-03T20:01:44Z
dc.date.issued2001-08
dc.identifier.otherliu_renyi_200108_ms
dc.identifier.urihttp://purl.galileo.usg.edu/uga_etd/liu_renyi_200108_ms
dc.identifier.urihttp://hdl.handle.net/10724/20226
dc.description.abstractMultiple sequence alignment plays a crucial role in extracting structural, functional, and evolutionary information from the exponentially growing sequence data from the ongoing genome sequencing. Based on the case study of retrotransposon sequence alignment, this thesis compares three alignment programs, DIALIGN, CLUSTALW, and PRRN, and proposes some strategies to improve alignment quality, such as realigning certain sequences or sequence ranges with different programs or parameters and hand editing. Entropy is used as an alignment quality indicator. This study also presents the design and development of an alignment tool, named AlignAgain, which is built to help biologists to improve alignment quality. AlignAgain is written in Java and allows users to display, edit, realign whole or partial sequences with CLUSTALW or PRRN, and append sequences with profile alignment.
dc.publisheruga
dc.rightspublic
dc.subjectMultiple sequence alignment
dc.subjectJava
dc.subjectClustalw
dc.subjectPrrn
dc.subjectGenomics
dc.subjectRetrotransposon
dc.subjectViewer
dc.subjectEditor
dc.titleStrategies for improving multiple alignment of retrotransposon sequences
dc.typeThesis
dc.description.degreeMS
dc.description.departmentComputer Science
dc.description.majorComputer Science
dc.description.advisorEileen T. Kraemer
dc.description.committeeEileen T. Kraemer
dc.description.committeeJohn A. Miller
dc.description.committeeWalter D. Potter


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