Title

A new Motzkin class for joint RNA secondary structures

Authors

Athanasios Alexiou*, Panayiotis Vlamos

Affiliation

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

Email

alexiou@ionio.gr; *Corresponding author

Article type

Hypothesis

Date

Received March 16, 2011; Accepted May 07, 2011; Published May 07, 2011

In general RNA prediction problem includes genetic mapping, physical mapping and structure prediction. The ultimate goal of structure prediction is to obtain the three dimensional structure of bimolecules through computation. The key concept for solving the above mentioned problem is the appropriate representation of the biological structures. Even though, the problems that concern representations of certain biological structures like secondary structures either are characterized as NP-complete or with high complexity, few approximation algorithms and techniques had been constructed, mainly with polynomial complexity, concerning the prediction of RNA secondary structures. In this paper, a new class of Motzkin paths is introduced, the so-called semi-elevated inverse Motzkin peakless paths for the representation of two interacting RNA molecules. The basic combinatorial interpretations on single RNA secondary structures are extended via these new Motzkin paths on two RNA molecules and can be applied to the prediction methods of joint structures formed by interacting RNAs.

Keywords

RNA-RNA interaction problem, RNA secondary Structures, semi-elevated Motzkin paths

Citation

Alexiou & Vlamos. Bioinformation 6(4): 162-163 (2011)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.