ABSTRACT

Many bioinformatics studies require the analysis of RNA structures. More specifically, extensive work is done to elaborate efficient algorithms able to predict the 2-D folding structures of RNA. The core of RNA structure is a dynamic programming algorithm to predict RNA secondary structures from sequence based on the principle of minimizing free energy. In this paper the thermodynamic data have been used for RNA predictions.
In this paper the free energy minimization and the partition function code has been used to predict internal loops of any size in O (N3) time. The free energy table for multibranch loops has been used by Dynalign. Base pair probabilities have been determined by the partition function calculation. Parameters controlling the prediction of suboptimal structures are Max % Energy Difference and Max Number of Structures. The fold module provides the basic implementation of RNA secondary structure prediction.
A Dynalign dot plot, a separate dot plot is generated for each of the two sequences involved. OligoScreen calculates the unimolecular and bimolecular folding free energies for a set of RNA oligonucleotides.