Publication Date

Spring 2011

Degree Type

Master's Project

Degree Name

Master of Science (MS)


Computer Science

First Advisor

Sami Khuri

Second Advisor

Chris Pollett

Third Advisor

Robert Fowler


Ribonucleic Acid (RNA) is one of the major macromolecules essential to all forms of life. Apart from the important role played in protein synthesis, it performs several important functions such as gene regulation, catalyst of biochemical reactions and modification of other RNAs. In some viruses, instead of DNA, RNA serves as the carrier of genetic information. RNA is an interesting subject of research in the scientific community. It has lead to important biological discoveries. One of the major problems researchers are trying to solve is the RNA structure prediction problem. It has been found that the structure of RNA is evolutionary conserved and it can help to determine the functions served by them. In this project, I will be developing a tool to predict the secondary structure of RNA using simulated annealing. The aim of this project is to understand in detail the simulated annealing algorithm and implement it to find solutions to RNA secondary structure. The results will be compared with the very famous tool Mfold, developed by Michael Zuker, using the minimum free energy approach.