Please use this identifier to cite or link to this item:
http://hdl.handle.net/20.500.11861/7462
Title: | Classification of RNA sequences with pseudoknots using features based on partial sequences |
Authors: | Tong, Kwok-Kit Cheung, Kwan-Yau Lee, Kin-Hong Prof. LEUNG Kwong Sak |
Issue Date: | 2015 |
Publisher: | IEEE |
Source: | 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB |
Journal: | 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, |
Abstract: | Classification on pseudoknots existence is a challenging and meaningful problem in Bioinformatics. As predicting RNA secondary structures with pseudoknots is NP-complete problem while predicting pseudoknot-free structures can be done in O(n 3 ) time, if a preliminary pseudoknots existence classification of RNA sequence can be done before the prediction, the classification result can enhance the efficiency of RNA secondary structure prediction. In this paper, a classification of the existence of pseudoknots in an RNA sequence is presented. A set of features have been chosen by partial sequence content and thousands of RNA sequences with validated structures are used to train the classifier. Using a validated testing dataset, this classification method is shown to achieve a very good performance that the best result get 87% accuracy in 10-fold cross validation and around 75% accuracy in testing data. Moreover it may reveal how partial sequence content can affect the formation of pseudoknots. |
Type: | Peer Reviewed Journal Article |
URI: | http://hdl.handle.net/20.500.11861/7462 |
ISBN: | 978-1-4799-6926-5 |
DOI: | 10.1109/CIBCB.2015.7300277 |
Appears in Collections: | Applied Data Science - Publication |
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