AlienG2 - An Automated Analysis Tool for Genome-scale Prediction of Horizontal Gene Transfer

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dc.contributor.advisorDing, Qinen_US
dc.contributor.authorAhmadvand, Alien_US
dc.contributor.departmentComputer Scienceen_US
dc.date.accessioned2014-01-28T12:52:47Z
dc.date.available2014-01-28T12:52:47Z
dc.date.issued2013en_US
dc.description.abstractThis thesis will present a method for predicting Horizontal Gene Transfer (HGT) events through the creation of a web-based application called AlienG2. HGT is the process of genetic exchange between distantly related organisms. The benefits and applications for identifying HGT are numerous and have been studied in depth, as well as the many techniques and related tools for identifying them. Each one of these tools has its own advantages and disadvantages; yet, there is still a need for a tool that may be used practically and that also delivers results in a relatively short turnaround.  AlienG2 consists of the combination of two already established methods, AlienG and PhyloGenie. AlienG is a sequence similarity comparison based tool that assumes that sequence similarity is correlated to phylogenetic relatedness. Although this tool is fast, the accuracy of the result could be improved. On the other hand, however, while PhyloGenie has been developed using phylogenetic techniques and is known to be the most precise technique for identifying HGT, its very long running time makes it practically unusable. In order to create AlienG2 both AlienG and PhyloGenie had to be improved and then combined. As another improvement to make it more easily accessible for its primary users, which are mostly biologists, this tool was created with Web Service architecture and as a web-based application. The results of experiments show drastic improvement in the running time of the tool, making it quite practical.  en_US
dc.description.degreeM.S.en_US
dc.format.extent63 p.en_US
dc.format.mediumdissertations, academicen_US
dc.identifier.urihttp://hdl.handle.net/10342/4295
dc.language.isoen_US
dc.publisherEast Carolina Universityen_US
dc.subjectComputer scienceen_US
dc.subjectAlienGen_US
dc.subjectHGTen_US
dc.subjectPhyloGenieen_US
dc.subjectPredictionen_US
dc.subjectToolen_US
dc.subject.lcshBioinformatics
dc.subject.lcshWeb applications
dc.subject.lcshGenetic transformation
dc.titleAlienG2 - An Automated Analysis Tool for Genome-scale Prediction of Horizontal Gene Transferen_US
dc.typeMaster's Thesisen_US

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