Linear Time Algorithm for Parsing RNA Secondary Structure

Abstract Baharak Rastegari and Anne Condon Department of Computer Science, University of British Columbia Abstract. Accurate prediction of pseudoknotted RNA secondary structure is an important computational challenge. Typical prediction algorithms aim to find a structure with minimum free energy according to some thermodynamic (“sum of loop energies”) model that is implicit in the recurrences of the algorithm. However, a clear definition of what exactly are the loops and stems in pseudoknotted structures, and their associated energies, has been lacking. We present a comprehensive classification of loops in pseudoknotted RNA secondary structures. Building on an algorithm of Bader et al. [2] we obtain a linear time algorithm for parsing a secondary structures into its component loops. We also give a linear time algorithm to calculate the free energy of a pseudoknotted secondary structure. This is useful for heuristic prediction algorithms which are widely used since (pseudoknotted...

• Type: Conference
• Year: 2005
• Where: WABI
• Authors: Baharak Rastegari, Anne Condon
• Keywords: Algorithms, Linear Time Algorithm, Rna Secondary Structure, Secondary Structure, WABI 2005