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      • HARVEST
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      Scrambling analysis of ciliates

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      Date
      2009-08
      Author
      Liu, Jing
      Type
      Thesis
      Degree Level
      Masters
      Metadata
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      Abstract
      Ciliates 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.
      Degree
      Master of Science (M.Sc.)
      Department
      Computer Science
      Program
      Computer Science
      Supervisor
      McQuillan, Ian
      Committee
      Kusalik, Tony; Keil, Mark; Wu, Fangxiang
      Copyright Date
      August 2009
      URI
      http://hdl.handle.net/10388/etd-09092009-154551
      Subject
      theoretical computer science
      ciliate scrambling system
      scrambling analysis
      sequence alignment
      bioinformatics
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      • Graduate Theses and Dissertations
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