| Summary: | 碩士 === 國立交通大學 === 資訊科學系 === 91 === RNA Secondary Structure Prediction by Genetic Programming
Student：Chao-I Chen Advisor：Yuh-Jyh Hu
Institute of Computer and Information Science
National Chiao Tung University
Hsinchu, Taiwan, Republic of China
ABSTRACT
In this study we apply genetic programming to a set of related RNA sequences to find their common RNA secondary structures. Our method contains two main procedures. At the first stage, we provide two different stem representations to extract all legal candidate stems on each sequence. Some of these stems are in common secondary structures. Next, genetic programming is used to optimize individuals in population. In this step, each individual representing common secondary structures is described by our structure representation, a flexible representation for all kinds of RNA secondary structures. We also propose a new fitness criterion other than free energy measure to evaluate common secondary structures. We had obtained satisfactory experimental results on six different RNA families including two pseudo-knot data sets. This web-based tool, Genetic Programming for RNA Motifs (GPRM), is available at http://bioinfo.cis.nctu.edu.tw/service/gprm/.
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