Computational Methods for RNA Secondary Structure Prediction

The function of an RNA is mostly related to it tertiary structure. These structures could be precisely determined by NMR or X-ray crystallography techniques, but it is very expensive and time consuming. Therefore, using the computational methods for predicting the RNA tertiary structure become attractive. Since the prediction of RNA tertiary structure is very complex and computationally inefficient, most of the researches are focus on the problems related to RNA secondary structures. This kind of structures could be described by a set of paired location in an RNA sequence. This problem has been introduced almost 30 years ago and many researches have been down to solve it. Minimizing the free energy is an important approach to attach it and based on this approach Nossinov and Zuker algorithms are devised. In this paper, basic concepts related to the RNA structures are introduced and the mentioned two algorithms are presented and analyzed in details.