In partial fulfillment of the Requirements for the Degree of
Master of Science
Charles Katili
will defend his thesis
Abstract
Sequencing projects have created a wealth of data including complete genomes for many microbial, viral, and eukaryotic organisms. Strong evidence supports that variations in statistical properties seen in different regions of a genome are correlated with its evolutionary and functional organization. Therefore, analysis of such properties is relevant to many ongoing biomedical research efforts.
Traditional methods for graphical representation for sequence comparison were designed specifically for relatively short sequences not those of genomic length. Consequently, when applied for large sequence comparison, many such methods meet with limited success sacrificing accuracy and/or speed. With genomic sequences in mind, a novel graphical approach for rapid large-scale comparison, analysis and visualization of genomic sequences has been developed. This tool, Similarity Plot or S-plot for short, provides a two dimensional representation of the statistical similarity between all regions of a user defined length from the two genomes being compared. S-plot calculates this similarity based on the correlation between distributions of short nucleotide subsequences present in each region.
With the aid of this tool useful information can be revealed regarding global genome organization in addition to evolution and function of various genomic regions. Regions of high similarity/dissimilarity, alignment, insertions, deletions, and repetition become clearly visible.
Date: Monday, April 29, 2004
Time: 3:00 PM
Place: 200-PGH
Faculty, students, and the general public are invited.
Thesis Advisor: Dr. Yuriy Fofanov