RNAbor: a web server for RNA structural neighbors

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W305-9. doi: 10.1093/nar/gkm255. Epub 2007 May 25.


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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cluster Analysis
  • Computational Biology / methods*
  • Computer Simulation
  • Conserved Sequence
  • Databases, Genetic
  • Internet
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • RNA, Untranslated
  • Regulatory Sequences, Ribonucleic Acid
  • Sequence Alignment
  • Sequence Analysis, RNA
  • Sequence Homology, Nucleic Acid


  • RNA, Untranslated
  • Regulatory Sequences, Ribonucleic Acid
  • RNA