ABSTRACT
Bioinformatics has evolved from its initial function of storage and maintenance of biological data repositories to include the present-day computational techniques to analyze biological data. Secondary structure identification of the RNA sequence is important in bioinformatics. RNA needs to perform its biological functions and give a lead for predicting the tertiary structure of RNA. The secondary structure of the RNA sequence is used for the design and testing of pharmaceutical products. This chapter dealt with the classification of RNA molecules and followed by its secondary structure prediction techniques. The standard methods are base pairing and energetics based secondary structure prediction techniques. The base pair mode of prediction is based on a stacked pair, hairpin loop, bulge loop, interior loop, and multi-loop. Nussinov algorithm is one of the base pair formulation techniques that developed as a software. In the energy minimization method, Gibbs free energy is considered for RNA structure formation. Zuker’s algorithm is such an algorithm developed as software for RNA secondary structure prediction.
