一种检测RNA H型假结的启发式方法。
A heuristic approach for detecting RNA H-type pseudoknots.
作者信息
Huang Chun-Hsiang, Lu Chin Lung, Chiu Hsien-Tai
机构信息
Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, Republic of China.
出版信息
Bioinformatics. 2005 Sep 1;21(17):3501-8. doi: 10.1093/bioinformatics/bti568. Epub 2005 Jun 30.
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
动机
RNA H型假结是普遍存在的假结，几乎在所有类型的RNA中都能找到，并被认为在多种生物学过程中发挥着非常重要的作用。检测这些RNA H型假结有助于我们更好地理解RNA结构及其相关功能。然而，目前现有的用于检测此类RNA H型假结的程序仍然耗时，有时甚至无效。因此，需要高效且有效的工具来检测RNA H型假结。
结果
在本文中，我们采用了一种启发式方法来开发一种名为HPknotter的新型工具，用于高效、准确地检测RNA序列中的H型假结。此外，我们通过对一些已知H型假结的序列进行测试，证明了HPknotter的适用性和有效性。我们的方法可以很容易地扩展并应用于其他更一般类型的假结。
可用性
我们的HPknotter网络服务器可在http://bioalgorithm.life.nctu.edu.tw/HPKNOTTER/ 进行在线分析。
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