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Title

Combinatorial permutation based algorithm for representation of closed RNA secondary structures

 

Authors

Athanasios T Alexiou*, Maria M Psiha, Panayiotis M Vlamos

 

Affiliation

Department of Informatics, Ionian University, Plateia Tsirigoti 7, 49100 Corfu, Greece

 

Email

alexiou@ionio.gr; *Corresponding author

 

Phone

+30 6944 551797

 

Fax

+30 210 953329697

 

Article Type

Prediction Model

 

Date

Received August 22, 2011; Accepted August 30, 2011; Published September 06, 2011

 

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

 

Citation

Alexiou et al. Bioinformation 7(2): 91-95 (2011)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

Copyright

Publisher

 

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

 

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.