Date of Award

Fall 2000

Degree Type

Thesis - Restricted

Degree Name

Master of Science (MS)


Mathematics, Statistics and Computer Science

First Advisor

Tonellato, Peter J.

Second Advisor

Clough, Anne V.

Third Advisor

Jacob, Howard J.


Expressed Sequence Tags (EST) are short DNA sequences derived from single pass sequencing of reverse transcribed RNA libraries. Together with other gene-derived sequences, ESTs are computationally clustered as UniGenes to represent the theoretical predictions of biological genes. The accuracy of gene homology analysis based on UniGene sequence similarity directly affects both the computational and wet lab methods that rely on the UniGenes and predicted homologs. In this study, the optimal DNA sequence alignment criteria for identification of orthologous UniGenes between rat and mouse and between mouse and human were systematically analyzed and determined. Furthermore, scoring algorithms designed to extract unique orthologous UniGene pairs from complex UniGene "objects" were implemented and tested in conjunction with the DNA sequence alignment criteria. The results from this study have been successfully applied to comparative gene mapping and analysis.