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Bioinformatics Advance Access originally published online on June 30, 2005
Bioinformatics 2005 21(17):3501-3508; doi:10.1093/bioinformatics/bti568
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

A heuristic approach for detecting RNA H-type pseudoknots

Chun-Hsiang Huang , Chin Lung Lu * and Hsien-Tai Chiu *

Department of Biological Science and Technology, National Chiao Tung University Hsinchu 300, Taiwan, Republic of China

*To whom correspondence should be addressed.

Motivation: RNA H-type pseudoknots are ubiquitous pseudoknots that are found in almost all classes of RNA and thought to play very important roles in a variety of biological processes. Detection of these RNA H-type pseudoknots can improve our understanding of RNA structures and their associated functions. However, the currently existing programs for detecting such RNA H-type pseudoknots are still time consuming and sometimes even ineffective. Therefore, efficient and effective tools for detecting the RNA H-type pseudoknots are needed.

Results: In this paper, we have adopted a heuristic approach to develop a novel tool, called HPknotter, for efficiently and accurately detecting H-type pseudoknots in an RNA sequence. In addition, we have demonstrated the applicability and effectiveness of HPknotter by testing on some sequences with known H-type pseudoknots. Our approach can be easily extended and applied to other classes of more general pseudoknots.

Availability: The web server of our HPknotter is available for online analysis at http://bioalgorithm.life.nctu.edu.tw/HPKNOTTER/

Contact: cllu{at}mail.nctu.edu.tw, chiu{at}cc.nctu.edu.tw

Received on April 26, 2005; revised on June 28, 2005; accepted on June 28, 2005

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