Skip Navigation

Nucleic Acids Research 2004 32(22):6636-6642; doi:10.1093/nar/gkh1008
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (240K) Freely available
Right arrow Supplementary Material
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 (5)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Hodas, N. O.
Right arrow Articles by Aalberts, D. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hodas, N. O.
Right arrow Articles by Aalberts, D. P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 17 December 2004

Nucleic Acids Research, Vol. 32 No. 22 © Oxford University Press 2004; all rights reserved

Articles

Efficient computation of optimal oligo–RNA binding

Nathan O. Hodas and Daniel P. Aalberts*

Physics Department, Williams College, Williamstown, MA 01267, USA

* To whom correspondence should be addressed. Tel: +1 413 597 3520; Fax: +1 413 597 4116; Email: aalberts{at}williams.edu

Received August 11, 2004; Revised October 2, 2004; Accepted November 30, 2004

We present an algorithm that calculates the optimal binding conformation and free energy of two RNA molecules, one or both oligomeric. This algorithm has applications to modeling DNA microarrays, RNA splice-site recognitions and other antisense problems. Although other recent algorithms perform the same calculation in time proportional to the sum of the lengths cubed, ((N1 + N2)3), our oligomer binding algorithm, called BINDIGO, scales as the product of the sequence lengths, (N1·N2). The algorithm performs well in practice with the aid of a heuristic for large asymmetric loops. To demonstrate its speed and utility, we use BINDIGO to investigate the binding proclivities of U1 snRNA to mRNA donor splice sites.


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
 BioinformaticsHome page
U. Muckstein, H. Tafer, J. Hackermuller, S. H. Bernhart, P. F. Stadler, and I. L. Hofacker
Thermodynamics of RNA-RNA binding
Bioinformatics, May 15, 2006; 22(10): 1177 - 1182.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. P. Aalberts, E. G. Daub, and J. W. Dill
Quantifying optimal accuracy of local primary sequence bioinformatics methods
Bioinformatics, August 15, 2005; 21(16): 3347 - 3351.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. P. Aalberts and N. O. Hodas
Asymmetry in RNA pseudoknots: observation and theory
Nucleic Acids Res., April 14, 2005; 33(7): 2210 - 2214.
[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.