Skip Navigation



Bioinformatics Advance Access published online on February 1, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl023
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/10/1172    most recent
btl023v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Hofacker, I. L.
Right arrow Articles by Stadler, P. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hofacker, I. L.
Right arrow Articles by Stadler, P. F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 5, 2005
Revised December 3, 2005
Accepted January 23, 2006

Article

Memory efficient folding algorithms for circular RNA secondary structures

Ivo L. Hofacker 1 * and Peter F. Stadler 2

1 Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria
2 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria; The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, New Mexico

* To whom correspondence should be addressed.
Ivo L. Hofacker, E-mail: ivo{at}tbi.univie.ac.at


  Abstract

Background: A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach is to compute circular structures from "internal" and "external" substructures separated by a base pair. This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only.

Result: Here we describe how circular secondary structures can be obtained without additional memory requirements as a kind of "post-processing" of the linear structures.

Availability: The circular folding algorithm is implemented in the current version of the of RNAfold program of the Vienna RNA Package, which can be downloaded from http://www.tbi.univie.ac.at/RNA/.

Associate Editor: Thomas Lengauer
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
 Genome ResHome page
J. Armisen, M. J. Gilchrist, A. Wilczynska, N. Standart, and E. A. Miska
Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis
Genome Res., October 1, 2009; 19(10): 1766 - 1775.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. A. Raker, A. A. Mironov, M. S. Gelfand, and D. D. Pervouchine
Modulation of alternative splicing by long-range RNA structures in Drosophila
Nucleic Acids Res., August 1, 2009; 37(14): 4533 - 4544.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
O. Ben-Ami, N. Pencovich, J. Lotem, D. Levanon, and Y. Groner
A regulatory interplay between miR-27a and Runx1 during megakaryopoiesis
PNAS, January 6, 2009; 106(1): 238 - 243.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. R. Gruber, R. Lorenz, S. H. Bernhart, R. Neubock, and I. L. Hofacker
The Vienna RNA Websuite
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W70 - W74.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
L. Nie, G. Wu, and W. Zhang
Correlation of mRNA Expression and Protein Abundance Affected by Multiple Sequence Features Related to Translational Efficiency in Desulfovibrio vulgaris: A Quantitative Analysis
Genetics, December 1, 2006; 174(4): 2229 - 2243.
[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.