A heuristic approach for detecting RNA H-type pseudoknots

  • Authors:

  • Chun-Hsiang Huang;Chin Lung Lu;Hsien-Tai Chiu

  • Affiliations:

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

  • Venue:
  • Bioinformatics
  • Year:
  • 2005

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Abstract

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@mail.nctu.edu.tw, chiu@cc.nctu.edu.tw