SARNA-Predict: A study of RNA secondary structure prediction using different annealing schedules

This paper presents an algorithm for RNA secondary structure prediction based on Simulated Annealing (SA) and also studies the effect of using different types of annealing schedules. SA is known to be effective in solving many different types of minimization problems and for being able to approximate global minima in the solution space. Based on free energy minimization techniques, this permutation-based SA algorithm heuristically searches. for the structure with a free energy value close to the minimum free energy Delta G for that strand, within given constraints. Other contributions of this paper include the use of permutation-based encoding for RNA secondary structure and the swap mutation operator. Also, a detailed study of the convergence behavior of the algorithm is conducted and various annealing schedules are investigated. An evaluation of the performance of the new algorithm in terms of prediction accuracy is made via comparison with the dynamic programming algorithm mfold for thirteen individual known structures from four RNA classes (5S rRNA, Group I intron 23 rRNA, Group I intron 16S rRNA and 16S rRNA). Although dynamic programming algorithms for RNA folding are guaranteed to give the mathematically optimal (minimum energy) structure, the fundamental problem of this approach seems to be that the thermodynamic model is only accurate within 5 - 10%. Therefore, it is difficult for a single sequence folding algorithm to resolve which of the plausible lowest-energy structure is correct. The new algorithm showed comparable results with mfold and demonstrated a slightly higher specificity.