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Nucleic Acids Research 2006 34(Web Server issue):W416-W422; doi:10.1093/nar/gkl210
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures

Yanga Byun and Kyungsook Han*

School of Computer Science and Engineering, Inha University Inchon 402-751, Korea

*To whom correspondence should be addressed. Tel: +82 32 860 7388; Fax: +82 32 863 4386; Email: khan{at}inha.ac.kr

Received February 14, 2006. Revised March 24, 2006. Accepted March 24, 2006.

Visualizing RNA secondary structures and pseudoknot structures is essential to bioinformatics systems that deal with RNA structures. However, many bioinformatics systems use heterogeneous data structures and incompatible software components, so integration of software components (including a visualization component) into a system can be hindered by incompatibilities between the components of the system. This paper presents an XML web service and web application program for visualizing RNA secondary structures with pseudoknots. Experimental results show that the PseudoViewer web service and web application are useful for resolving many problems with incompatible software components as well as for visualizing large-scale RNA secondary structures with pseudoknots of any type. The web service and web application are available at http://pseudoviewer.inha.ac.kr/.


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