RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

RNA. 2012 Jul;18(7):1319-27. doi: 10.1261/rna.032052.111. Epub 2012 May 29.


Automated RNA alignment algorithms often fail to recapture the essential conserved sites that are critical for function. To assist in the refinement of these algorithms, we manually curated a set of 148 alignments with a total of 9600 unique sequences, in which each alignment was backed by at least one crystal or NMR structure. These alignments included both naturally and artificially selected molecules. We used principles of isostericity to improve the alignments from an average of 83%-94% isosteric base pairs. We expect that this alignment collection will assist in a wide range of benchmarking efforts and provide new insight into evolutionary principles governing change in RNA structural motifs. The improved alignments have been contributed to the Rfam database.

Publication types

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

MeSH terms

  • Algorithms
  • Base Sequence
  • Databases, Nucleic Acid*
  • Evolution, Molecular*
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Nucleotide Motifs
  • RNA / chemistry*
  • Sequence Alignment*


  • RNA