Finding Patterns in DNA Sequences through Visualization with Symbolic Scatter Plots

Visualization is frequently mentioned as a technique for analyzing large amounts of data. It has been widely anticipated for many years that visualization would become a major tool for the analysis of rapidly growing genomic databases. However, beyond the dot plot which was introduced in 1981 there have been few successful attempts at visualizing this data. In this thesis a new technique for visualizing DNA sequences, the symbolic scatter plot, is introduced. It is shown how the symbolic scatter plot addresses the problems of 1) finding complex patterns in DNA sequences and 2) the comparison of sequences. Second, the symbolic scatter plot is analyzed in terms of human visual perception – particularly in terms of Gestalt theory and pre-attentive visual processing. Third, examples of how specific pre-attentive visual cues can be manipulated or added to find motifs and visualize information content (i.e. entropy) are presented. Fourth, the practicality of symbolic scatter plots is demonstrated by using them to visualize and compare the human and chimpanzee genes responsible for Huntington’s disease.

Author dc:creator

• Cox, David

Advisors dc:contributor.advisor

• Alan L Tharp, Committee Chair
• Steffen Heber, Committee Member
• Christopher G Healey, Committee Member
• Donald L Bitzer, Committee Member

• pattern finding
• visualization
• symbolic scatter plots
• DNA sequences

Statement dc:rights

• I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dis sertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to NC State University or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.

Dc Identifier Other

etd-03012010-210719

OAI record oai:identifier

https://repository.lib.ncsu.edu/server/oai/request?verb=GetRecord&metadataPrefix=dim&identifier=oai%3Arepository.lib.ncsu.edu%3A1840.16%2F6264