Multi-syllabic DNA motif discovery
Author(s)
Kumar, Rasika S
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Alternative title
Multi-syllabic deoxyribonucleic acid motif discovery
Other Contributors
Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.
Advisor
David Gifford.
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This paper describes a method for finding multi-syllabic motifs in a genome. It expands on the algorithm developed by Takusagawa, et al[1, 2] that uses data from Chromatin Immuno-Precipitation (ChIP) experiments to isolate regions that have a given motif. The Takusagawa method uses an enumeration method to search for motifs in both positive and negative intergenic regions in order to determine the statistical significance of the results. Our algorithm also uses enumeration to find motifs that have gaps between the different sub-motifs, or syllables. This thesis also describes a method to calculate the significance of each motif and tests this method via Monte Carlo simulations on random test sets. The significant motifs found using this algorithm are verified against consensus motifs found in the literature.
Description
Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005. Includes bibliographical references (leaves 75-78).
Date issued
2005Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer SciencePublisher
Massachusetts Institute of Technology
Keywords
Electrical Engineering and Computer Science.