A Memory Efficient Algorithm for Structural Alignment of RNAs with Embedded Simple Pseudoknots

In this paper, we consider the problem of structural alignment of a target RNA sequence of length n and a query RNA sequence of length m with known secondary structure that may contain embedded simple pseduoknots. The best known algorithm for solving this problem (Dost et al. [13]) runs in O(mn4) time with space complexity of O(mn3), which requires too much memory making it infeasible for comparing ncRNAs (non-coding RNAs) with length several hundreds or more. We propose a memory efficient algorithm to solve the same problem. We reduce the space complexity to O(mn2 + n3) while maintaining the same time complexity of Dost et al.’s algorithm. Experimental reslts show that our algorithm is feasible for comparing ncRNAs of length more than 500. Availability: The source code of our program is available upon request.