Rastegari, Baharak and Condon, Anne (2005) Linear time algorithm for parsing RNA secondary structure. In, Casadio, R. and Myers, G. (eds.) Algorithms in Bioinformatics. WABI 2005. (Lecture Notes in Computer Science: Algorithms in Bioinformatics, 3692) Berlin; Heidelberg. Springer, pp. 341-352. (doi:10.1007/11557067_28).
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. 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) RNA secondary structure prediction is NP-hard. Finally, we give a linear time algorithm to test whether a secondary structure is in the class handled by Akutsu’s algorithm. Using our tests, we analyze the generality of Akutsu’s algorithm for real biological structures.
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