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A System for Determining the Statistical Significance of the Frequency of Short DNA Motif Matches in a Genome - An Analytical Approach

Pfeiffer, Philip Edward
http://rave.ohiolink.edu/etdc/view?acc_num=dayton1304599225

Abstract Details

2011, Master of Computer Science (M.C.S.), University of Dayton, Computer Science.
A problem in biology arises in the evaluation of statistical significance of the observed frequency of candidate transcription factor binding site matches (To) in a genome. This is because possible overlaps in the genome render the usual chi-square test unsuitable. In this study, we develop generalized models for evaluating the expectation and variance of T over a variety of probability spaces of randomly occurring sequences of elements (or symbols), which can then be used to perform a Z test. In addition, a software toolset in Java was developed to implement basic tools for manipulating molecular sequences along with code for implementing the discovery algorithm and the statistical tools for each of the probability models considered. These Sequence tools are then included in a proposed design to develop a workbench to discover sequence motifs in a genome.
Sudhindra Gadagkar, PhD (Committee Chair)
Jenifer Seitzer, PhD (Committee Co-Chair)
James Buckley, PhD (Committee Member)
Dale Courte, PhD (Committee Member)
Peter Hovey, PhD (Committee Member)
56 p.
Bioinformatics; Computer Science; Mathematics; Statistics
probability models; DNA; motifs; JAVA; sequence software

Recommended Citations

Citations

  • Pfeiffer, P. E. (2011). A System for Determining the Statistical Significance of the Frequency of Short DNA Motif Matches in a Genome - An Analytical Approach [Master's thesis, University of Dayton]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1304599225

    APA Style (7th edition)

  • Pfeiffer, Philip. A System for Determining the Statistical Significance of the Frequency of Short DNA Motif Matches in a Genome - An Analytical Approach. 2011. University of Dayton, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=dayton1304599225.

    MLA Style (8th edition)

  • Pfeiffer, Philip. "A System for Determining the Statistical Significance of the Frequency of Short DNA Motif Matches in a Genome - An Analytical Approach." Master's thesis, University of Dayton, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1304599225

    Chicago Manual of Style (17th edition)

dayton1304599225
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© 2011, all rights reserved.
This open access ETD is published by University of Dayton and OhioLINK.