Skip Navigation


Bioinformatics Advance Access originally published online on June 30, 2005
Bioinformatics 2005 21(17):3501-3508; doi:10.1093/bioinformatics/bti568
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/17/3501    most recent
bti568v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (4)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Huang, C.-H.
Right arrow Articles by Chiu, H.-T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Huang, C.-H.
Right arrow Articles by Chiu, H.-T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 RNAHome page
J. Sperschneider and A. Datta
KnotSeeker: Heuristic pseudoknot detection in long RNA sequences
RNA, April 1, 2008; 14(4): 630 - 640.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y.-S. Chung, W.-H. Lee, C. Y. Tang, and C. L. Lu
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W639 - W644.
[Abstract] [Full Text] [PDF]

Home page
 J. Gen. Virol.Home page
M. L. Nibert
'2A-like' and 'shifty heptamer' motifs in penaeid shrimp infectious myonecrosis virus, a monosegmented double-stranded RNA virus
J. Gen. Virol., April 1, 2007; 88(4): 1315 - 1318.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.