NDLI: Approximating algorithm for RNA structure prediction including pseudoknots

Content Provider	IEEE Xplore Digital Library
Author	Zhendong Liu Yuxiao Dong Hengwu Li Huijian Han
Copyright Year	2011
Description	Author affiliation: School of Computer Science and Technology, Shandong Economic University, Jinan, 250014, Shandong Province, China (Hengwu Li; Huijian Han) \|\| School of Computer Science and Technology, Shandong Jianzhu University, Jinan, 250101 Shandong Province, China (Zhendong Liu; Yuxiao Dong)
Abstract	RNA structure and tertiary structure could be represented by a set of nested arcs and a set of crossing arcs. Based on the relative stability of the stems in RNA molecules, an approximating algorithm is presented to predict RNA pseudoknotted structure, the algorithm takes $O(n^{3})$ time and O(n) space, the algorithm outperforms other known algorithms in predicting accuracy. This algorithm not only reduces the time complexity to $O(n^{3}),$ but also widens the maximum length of the sequence. The preliminary experimental test on the RNA subsequences in PseudoBase confirm that the algorithm has good sensitivity and specificity, and are among the most reasonable in the literature.
Starting Page	325
Ending Page	329
File Size	705939
Page Count	5
File Format	PDF
ISBN	9781457703010
ISSN	2161816X
e-ISBN	9781457703027
e-ISBN	9781457703003
DOI	10.1109/ICAL.2011.6024736
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-08-15
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Algorithm design and analysis Accuracy RNA Heuristic algorithms Approximating algorithm Prediction algorithms Approximation algorithms NP-complete Complexity theory RNA structure Stem
Content Type	Text
Resource Type	Article

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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