Freyhult, E., Moulton, V. and Clote, P. (2007) RNAbor: a web server for RNA structural neighbors. Nucleic Acids Research, 35 (suppl 2). W305-W309. ISSN 0305-1048

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Abstract

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 d-neighbors of a given input RNA sequence and structure (the structure can, for example, be the minimum free energy (MFE) structure). A d-neighbor is a structure that differs from the input structure by exactly d base pairs, that is, it can be obtained from the input structure by adding and/or removing exactly d base pairs. For each distance d RNAbor computes the density of d-neighbors, the number of d-neighbors, and the MFE structure, or MFE d structure, among all d-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.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Computing Sciences
Related URLs:	http://dx.doi.org/10.1093/nar/gkm255
Depositing User:	Vishal Gautam
Date Deposited:	16 May 2011 17:20
Last Modified:	21 Apr 2020 19:23
URI:	https://ueaeprints.uea.ac.uk/id/eprint/23642
DOI:	10.1093/nar/gkm255

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