A predicting algorithm of RNA secondary structure based on stems
Abstract
Purpose
The purpose of this paper is to design an algorithm to predict RNA secondary structure, compared with other relevant algorithm, its time complexity and space complexity are reduced.
Design/methodology/approach
The dynamic programming algorithm need more time and space; it is very difficult to predict the RNA secondary structure which have more 1,000 bases. The nested RNA secondary structure algorithms cannot predict the RNA secondary structure containing pseudoknots, so the fast algorithm is needed to predict the RNA secondary structure containing pseudoknots urgently. Based on the greedy principle, a model is designed to solve the problem.
Findings
A greedy algorithm is presented to predict RNA secondary structure.
Research limitations/implications
The problem for predicting RNA secondary structure including pseudoknots is NP‐complete.
Practical implications
The paper presents a valuable and useful method for predicting the RNA secondary structure.
Originality/value
The new algorithm needs O(n3) time and O(n) space; the experimental results indicate that the algorithm has good accuracy and sensitivity.
Keywords
Citation
Liu, Z., Li, H. and Zhu, D. (2010), "A predicting algorithm of RNA secondary structure based on stems", Kybernetes, Vol. 39 No. 6, pp. 1050-1057. https://doi.org/10.1108/03684921011046825
Publisher
:Emerald Group Publishing Limited
Copyright © 2010, Emerald Group Publishing Limited