Combinatorial permutation based algorithm for representation of closed RNA secondary structures

Bioinformation. 2011;7(2):91-5. doi: 10.6026/97320630007091. Epub 2011 Sep 6.

Abstract

A permutation-based algorithm is introduced for the representation of closed RNA secondary structures. It is an efficient 'loopless' algorithm, which generates the permutations on base-pairs of 'k-noncrossing' setting partitions. The proposed algorithm reduces the computational complexity of known similar techniques in O(n), using minimal change ordering and transposing of not adjacent elements.

Keywords: Closed RNA secondary structures; k-noncrossing partitions; permutation-based algorithm.