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Nucleic Acids Res. 2007 Jul;35(Web Server issue):W305-9. Epub 2007 May 25.

RNAbor: a web server for RNA structural neighbors.

Author information

1
Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden.

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 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.

PMID:
17526527
PMCID:
PMC1933207
DOI:
10.1093/nar/gkm255
[Indexed for MEDLINE]
Free PMC Article

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