Multi-syllabic DNA motif discovery

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.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2005

Author dc:creator

• Kumar, Rasika S

Advisor dc:contributor.advisor

• David Gifford.

• Electrical Engineering and Computer Science.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/36789

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/36789