Combinatorial permutation based algorithm for representation of closed RNA secondary structures.

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.

SUBMITTER: Alexiou AT 

PROVIDER: S-EPMC3174042 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature