Scrambling analysis of ciliates

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.

Name thesis:degree_name

Master of Science (M.Sc.)

Level thesis:degree_level

Masters

Discipline thesis:degree_discipline

Computer Science

Grantor

University of Saskatchewan

Year dc:date.issued

2009

Author dc:creator

• Liu, Jing

Advisor dc:contributor.advisor

• McQuillan, Ian

Committee members dc:contributor.committeemember

• Kusalik, Tony
• Keil, Mark
• Wu, Fangxiang

• theoretical computer science
• ciliate scrambling system
• scrambling analysis
• sequence alignment
• bioinformatics

Language dc:language.iso

en_US

Handle dc:identifier.uri

https://hdl.handle.net/10388/etd-09092009-154551

OAI identifier oai:identifier

oai:harvest.usask.ca:10388/etd-09092009-154551