RNADPCompare: An algorithm for comparing RNA secondary structures based on image processing techniques

In structural biology, structural chemistry, and bioinformatics, Ribonucleic Acid (RNA) structure comparison is a fundamental problem. It is because structural comparison can facilitate RNA structure prediction and studies in RNA energy landscapes and conformational switches as well. There are many different tools have been proposed for RNA secondary structure comparison. This paper describes and presents a novel algorithm, RNADPCompare, for computing similarity measure of RNA secondary structures. The main idea for this algorithm is to represent the RNA secondary structure as a dot plot, and then process the dot plot as an image. The algorithm will utilize image processing techniques and heuristic understanding of the image properties to compute similarity measure of RNA secondary structures. Since many evolutionary and machine learning algorithms for RNA secondary structure design and prediction rely on good metric for examining structural similarities, therefore this novel metric will make significant contribution to the advances to these algorithms. An evaluation of the algorithm in terms of correlation to the native structure is made. The results from the six sequences of RNA from a variety of sequence lengths and organisms were tested. When comparing with Sfold, the prediction accuracy of using RNADPCompare to compute the difference matrix seems to be very promising. These results demonstrated that RNADPCompare is highly competitive in terms of the processing speed and accuracy when compare to other methods. This supports the use of this algorithm on other research in RNA secondary structure design and prediction.