Computational RNA secondary structure design: empirical complexity and improved methods

Background: We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various classes of RNA structures as the size of the target structure is increased. The purpose of this work is to understand better the factors that make RNA structures hard to design for existing, high-performance algorithms. Such understanding provides the basis for improving the performance of one of the best algorithms for this problem, RNA-SSD, and for characterising its limitations. Results: To gain insights into the practical complexity of the problem, we present a scaling analysis on random and biologically motivated structures using an improved version of the RNA-SSD algorithm, and also the RNAinverse algorithm from the Vienna package. Since primary structure constraints are relevant for designing RNA structures, we also investigate the correlation between the number and the location of the primary structure ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Rosalía Aguirre-Hernández, Holger H. Hoos, Anne Condon
• Keywords: Algorithms, BMCBI 2007, RNA Structures, RNA-SSD Algorithm