Novel representation of RNA secondary structure used to improve prediction algorithms |
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Authors: | Zou Q Lin C Liu X-Y Han Y-P Li W-B Guo M-Z |
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Institution: | School of Information Science and Technology, Xiamen University, Xiamen, China. |
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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. |
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