Q. Zou, C. Lin, X.-Y. Liu, Y.-P. Han, W.-B. Li and M.-Z. Guo
Genet. Mol. Res. 10 (3): 1986-1998 (2011)
Published: September 9, 2011
DOI: http://dx.doi.org/10.4238/vol10-3gmr1181

Cite this Article:
Q. Zou, C. Lin, X.-Y. Liu, Y.-P. Han, W.-B. Li and M.-Z. Guo (2011). A novel representation of RNA secondary structure and its application in comparative sequence analysis. Genet. Mol. Res. 10(3): 1986-1998. http://dx.doi.org/10.4238/vol10-3gmr1181

About the Authors:
Q. Zou, C. Lin, X.-Y. Liu, Y.-P. Han, W.-B. Li and M.-Z. Guo
Corresponding author: M.-Z. Guo
E-mail: maozuguo@hit.edu.cn

ABSTRACT:
We propose a novel representation of RNA secondary structure for a quick comparison of different structures. Secondary structure was viewed as a set of stems and each stem was represented by two values according to its position. Using this representation, we improved the comparative sequence analysis method results and the minimum free-energy model. In the comparative sequence analysis method, a novel algorithm independent of multiple sequence alignment was developed to improve performance. When dealing with a single-RNA sequence, the minimum free-energy model is improved by combining it with RNA class information. Secondary structure prediction experiments were done on tRNA and RNAse P RNA; sensitivity and specificity were both improved. Furthermore, software programs were developed for non-commercial use.

Key words: RNA secondary structure; Dot plots; Stem; Comparative sequence analysis.