Skip Navigation


Bioinformatics Advance Access originally published online on August 11, 2009
Bioinformatics 2009 25(20):2646-2654; doi:10.1093/bioinformatics/btp481
This Article
Right arrow Full Text
Right arrow Full Text (Print PDF)
Right arrow Supplementary Data
Right arrow All Versions of this Article:
25/20/2646    most recent
btp481v1
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 Huang, F. W. D.
Right arrow Articles by Stadler, P. F.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Huang, F. W. D.
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 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Partition function and base pairing probabilities for RNA–RNA interaction prediction

Fenix W. D. Huang 1, Jing Qin 1, Christian M. Reidys 1,2,* and Peter F. Stadler 3–7

1 Center for Combinatorics, LPMC-TJKLC, 2 College of Life Science, Nankai University Tianjin 300071, P.R. China, 3 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, 4 Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 5 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstraße 1,D-04103 Leipzig, Germany, 6 Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria and 7 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, USA

* To whom correspondence should be addressed.


  Abstract

Motivation: The RNA–RNA interaction problem (RIP) consists in finding the energetically optimal structure of two RNA molecules that bind to each other. The standard model allows secondary structures in both partners as well as additional base pairs between the two RNAs subject to certain restrictions that ensure that RIP is solvabale by a polynomial time dynamic programming algorithm. RNA–RNA binding, like RNA folding, is typically not dominated by the ground state structure. Instead, a large ensemble of alternative structures contributes to the interaction thermodynamics.

Results: We present here an O(N6) time and O(N4) dynamics programming algorithm for computing the full partition function for RIP which is based on the combinatorial notion of ‘tight structures’. Albeit equivalent to recent work by H. Chitsaz and collaborators, our approach in addition provides a full-fledged computation of the base pairing probabilities, which relies on the notion of a decomposition tree for joint structures. In practise, our implementation is efficient enough to investigate, for instance, the interactions of small bacterial RNAs and their target mRNAs.

Availability: The program rip is implemented in C. The source code is available for download from http://www.combinatorics.cn/cbpc/rip.html and http://www.bioinf.uni-leipzig.de/Software/rip.html.

Contact: duck{at}santafe.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Ivo Hofacker

Received on April 16, 2009; revised on June 21, 2009; accepted on August 2, 2009

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.