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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