Novel representation of RNA secondary structure used to improve prediction algorithms

Q. Zou, C. Lin, X.-Y. Liu, Y.-P. Han, W.-B. Li, M.-Z. Guo
2011 Genetics and Molecular Research  
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.
more » ... 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.
doi:10.4238/vol10-3gmr1181 pmid:21948761 fatcat:fzy7xe3gpvd77pps32sariuvdi