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Scrambling analysis of ciliates

dc.contributor.advisorMcQuillan, Ianen_US
dc.contributor.committeeMemberKusalik, Tonyen_US
dc.contributor.committeeMemberKeil, Marken_US
dc.contributor.committeeMemberWu, Fangxiangen_US
dc.creatorLiu, Jingen_US 2009en_US
dc.description.abstractCiliates are a class of organisms which undergo a genetic process called gene descrambling after mating. In order to better understand the problem, a literature review of past works has been presented in this thesis. This includes a brief summary of both the relevant biology and bioinformatics literature. Then, a formal definition of scrambling systems is developed which attempts to model the problem of sequence alignment between scrambled and descrambled genes. With this system, sequences can be classified into relevant functional segments. It also provides a framework whereby we can compare various ciliate sequence alignment algorithms. After that, a new method of predicting the various functional segments is studied. This method shows better coverage, and usually a better labelling score with certain parameters. Then we discuss several recent hypotheses as to how ciliates naturally descramble genes. An algorithm suite is developed to test these hypotheses. With the tests, we are able to computationally check which factors are potentially the most important. According to the current results with 247 pointer sequences of 13 micronuclear genes, examining repeats which are the same distance together with either the sequence or the size, as the real pointers, is almost always enough information to guide descrambling. Indeed, the real pointer sequence is the unique repeat 92.7% and 94.3% of the time within the 247 pointers, from the left and right respectively, using only the pointer distance and the pointer sequence information.en_US
dc.subjecttheoretical computer scienceen_US
dc.subjectciliate scrambling systemen_US
dc.subjectscrambling analysisen_US
dc.subjectsequence alignmenten_US
dc.titleScrambling analysis of ciliatesen_US
dc.type.materialtexten_US Scienceen_US Scienceen_US of Saskatchewanen_US of Science (M.Sc.)en_US


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