Date of Award

Fall 2007

Project Type


Program or Major

Computer Science

Degree Name

Master of Science

First Advisor

R Daniel Bergeron

Second Advisor

Vaughn S Cooper


We describe three software tools related to research in comparative genomics, a growing research area that explores the variation within and between organisms. We developed a set of tools that explore sequence similarity and differences in genomes. Two of these tools are specifically aimed at examining DNA sequence data from two or more genomes: (1) The Magenta's OPUS tool compares genomic sequences to identify shared or unique segments between closely related species. This tool looks for functional similarities and differences in genomic data by classifying sequences into groups based on genomic categories: Orthologs, Paralogs, and Unique Sequence. (2) The DSNP tool looks at the nucleotide level to find single nucleotide polymorphisms (SNPs) within an individual. This program is a collection of existing and custom built tools to discover and analyze SNPs within the Daphnia pulex genome. (3) The third tool supports a user evaluation of two different visualization techniques for comparing nucleotide or protein sequences.