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Ph.D. Theses

A Computational System for Identifying Cis-Regulatory Elements in Closely Related Genomes

By Thomas M. Smith
Advisors: Lee A. Newberg, Mukkai S. Krishnamoorthy
April 18, 2006

This thesis aims to provide a computational system for identifying cis-regulatory elements in closely related genomes. As a demonstration, an analysis of potential cis-regulatory elements in E. coli and related bacterial genomes is provided. Previous computational methods for such an analysis are somewhat ineffective because the species are closely related. This closeness causes statistical problems due to the high correlation between the sequence data in the genomes.

Methods for discovering potential cis-regulatory elements from DNA sequence data are reviewed, and a new computational method is demonstrated to address the correlation problem by accounting for evolutionary distances between species. A new software system is also shown to provide a computational platform necessary for more complex, collaborative analyses in the future.

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