In the study of RNA, an important task is finding the structural similarities and differences of two molecules. As the number of 3D structures available has been increasing dramatically in the past decade, it has become important and necessary for automated methods of RNA structural comparisons to be developed. Some RNA molecules, such as ribosomal RNA, consist of hundreds or even thousands of nucleotides, making such a task computationally difficult. A method of RNA 3D alignment using a simulated annealing based approach that involves discrete time Markov chains has been developed and is presented. Resulting alignments are compared with those produced by other algorithms that are currently widely used.

simulated annealing, RNA, alignment.