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Molecules 2018, 23(3), 697; https://doi.org/10.3390/molecules23030697

Feature-Based and String-Based Models for Predicting RNA-Protein Interaction

1
Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26508, USA
2
Faculty of Software, Fujian Normal University, Fuzhou 350108, China
3
McIntire School of Commerce, University of Virginia, Charlottesville, VA 22904, USA
4
McGovern Medical School, and School of Biomedical Informatics, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA
A shorter version of this work was presented at ACM BCB’17, August 2017, Boston, MA, USA.
*
Author to whom correspondence should be addressed.
Received: 21 December 2017 / Revised: 17 February 2018 / Accepted: 21 February 2018 / Published: 19 March 2018
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Abstract

In this work, we study two approaches for the problem of RNA-Protein Interaction (RPI). In the first approach, we use a feature-based technique by combining extracted features from both sequences and secondary structures. The feature-based approach enhanced the prediction accuracy as it included much more available information about the RNA-protein pairs. In the second approach, we apply search algorithms and data structures to extract effective string patterns for prediction of RPI, using both sequence information (protein and RNA sequences), and structure information (protein and RNA secondary structures). This led to different string-based models for predicting interacting RNA-protein pairs. We show results that demonstrate the effectiveness of the proposed approaches, including comparative results against leading state-of-the-art methods. View Full-Text
Keywords: RNA Protein Interaction; RPI; k-mers; suffix trees; richness; protein structure; RNA structure RNA Protein Interaction; RPI; k-mers; suffix trees; richness; protein structure; RNA structure
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Adjeroh, D.; Allaga, M.; Tan, J.; Lin, J.; Jiang, Y.; Abbasi, A.; Zhou, X. Feature-Based and String-Based Models for Predicting RNA-Protein Interaction. Molecules 2018, 23, 697.

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