Skip Navigation


Nucleic Acids Research Advance Access originally published online on May 25, 2007
Nucleic Acids Research 2007 35(Web Server issue):W305-W309; doi:10.1093/nar/gkm255
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1707K) Freely available
Right arrow Screen PDF (273K) Freely available
Right arrowOA All Versions of this Article:
35/suppl_2/W305    most recent
gkm255v1
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 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 Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Freyhult, E.
Right arrow Articles by Clote, P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Freyhult, E.
Right arrow Articles by Clote, P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W305-W309
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

RNAbor: a web server for RNA structural neighbors

Eva Freyhult1, Vincent Moulton2 and Peter Clote3,*

1Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden, 2School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK and 3Department of Biology, Boston College, Chestnut Hill, MA 02467, USA

*To whom correspondence should be addressed. Tel: + 1 617 552 1332; Fax: + 1 617 552 2011; Email: clote{at}bc.edu

Received January 24, 2007. Revised March 26, 2007. Accepted April 8, 2007.

RNAbor provides a new tool for researchers in the biological and related sciences to explore important aspects of RNA secondary structure and folding pathways. RNAbor computes statistics concerning {delta}-neighbors of a given input RNA sequence and structure (the structure can, for example, be the minimum free energy (MFE) structure). A {delta}-neighbor is a structure that differs from the input structure by exactly {delta} base pairs, that is, it can be obtained from the input structure by adding and/or removing exactly {delta} base pairs. For each distance {delta} RNAbor computes the density of {delta}-neighbors, the number of {delta}-neighbors, and the MFE structure, or MFE {delta} structure, among all {delta}-neighbors. RNAbor can be used to study possible folding pathways, to determine alternate low-energy structures, to predict potential nucleation sites and to explore structural neighbors of an intermediate, biologically active structure. The web server is available at http://bioinformatics.bc.edu/clotelab/RNAbor.


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
 Nucleic Acids ResHome page
J. Waldispuhl, S. Devadas, B. Berger, and P. Clote
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W281 - W286.
[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.