Date of Award

Spring 5-31-2004

Document Type


Degree Name

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


Computer Science

First Advisor

Michael Recce

Second Advisor

Barry Cohen

Third Advisor

Qun Ma


Pseudoknots are structures that are formed from the base pairing of an RNA secondary loop structure with a complementary base which lies somewhere outside of the loop. The result is a structure, which plays a vital role in cell structure rigidity, regulation of protein synthesis, and in the structural organization of RNA complexes. Deciphering RNA folding patterns would begin to unravel some of the mysteries surrounding the cell and its functions and open a new world to scientists. Many algorithms have been written in this quest to predict RNA's secondary structure but not many have been very successful.

In this thesis, some of these algorithms are discussed and considered for their strengths and weaknesses. First those algorithms, which exclude pseudoknots and other more complex structures, are presented. The later algorithms include those, which attempt to include some of the more complex structures into their calculations.

In the end, all the algorithms are taken into consideration and their strengths and weaknesses compared so as to find some path for future direction. By using the strengths found in these variety of algorithms and avoiding some of the piffalls encountered by others hopefully new algorithms will be developed in the future that are more successful in deciphering RNA secondary structure.