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An RNA secondary structure prediction method based on minimum and suboptimal free energy structures. (English) Zbl 1343.92377
Summary: The function of an RNA-molecule is mainly determined by its tertiary structures. And its secondary structure is an important determinant of its tertiary structure. The comparative methods usually give better results than the single-sequence methods. Based on minimum and suboptimal free energy structures, the paper presents a novel method for predicting conserved secondary structure of a group of related RNAs. In the method, the information from the known RNA structures is used as training data in a SVM (support vector machine) classifier. Our method has been tested on the benchmark dataset given by T. Puton et al. [“CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction”, Nucl. Acid. Res. 41, No. 7, 4307–4323 (2013; doi:10.1093/nar/gkt101)]. The results show that the average sensitivity of our method is higher than that of other comparative methods such as CentroidAlifold, MXScrana, RNAalifold, and TurboFold.
92D20 Protein sequences, DNA sequences
68T05 Learning and adaptive systems in artificial intelligence
Full Text: DOI
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