Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
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 Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Nakaya, A.
Right arrow Articles by Yonezawa, A.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Nakaya, A.
Right arrow Articles by Yonezawa, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© Oxford University Press

Visualization of RNA secondary structures using highly parallel computers

Akihiro Nakaya , Kenjiro Taura , Kenji Yamamoto 1 and Akinori Yonezawa *

Department of Information Science, Faculty of Science University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan
1Department of Bacteriology, Faculty of Medicine, University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan

* To whom correspondence should be addressed. E-mail:yonezawa{at}is.s.u-tokyo.ac.jp

Results of RNA secondary structure prediction algorithm are usually given as a set of hydrogen bonds between bases. However, we cannot know the precise structure of an RNA molecule by only knowing which bases form hydrogen bonds. One way to understand the structure of an RNA molecule is to visualize it using a planar graph so that we can easily know the geometric relations among the substructures such as stacking regions and loops. To do this, we consider bases to be particles on a plane and introduce a repulsive force and an attractive force among these particles and determine their positions according to these forces. A naive algorithm requires O(N2) time but we can reduce it to O(NlogN) with an approximation algorithm which is often used in the area of N-body simulation. Our program is written in parallel object-oriented language ‘Schematic’ which is recently developed. Efficiency of our implementation on a parallel computer and results of visualization of secondary structures are presented using cadang-cadang coconut viroid as an example.

Received on January 24, 1996; revised on May 13, 1996; accepted on May 13, 1996

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




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.