Document Type


Date of Award

Spring 5-31-2011

Degree Name

Master of Science in Bioinformatics - (M.S.)


Computer Science

First Advisor

Usman W. Roshan

Second Advisor

Zhi Wei

Third Advisor

Jason T. L. Wang


The key requirements of a good sequence alignment tool are high accuracy and fast execution. The existing Probalign program is a highly accurate tool for sequence alignment of both proteins and nucleotides. However, the time for execution is fairly high. The focus is therefore, to reduce the running time of the existing version of Probalign, maintaining its current accuracy level.

The thesis conducts a detail analysis of the performance of Probalign to bring down the running time of the existing code. A modified version of Probalign, Version 1.4 is released. A new program for sequence alignment with faster computation is also introduced.