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

J. Widmann, J. Stombaugh, D. Mcdonald, J. Chocholousova, P. Gardner, M.K. Iyer, Z.Z. Liu, C.A. Lozupone, J. Quinn, S. Smit, S. Wikman, J.R.R. Zaneveld, R. Knight

Research output: Contribution to journalArticleAcademicpeer-review

18 Citations (Scopus)

Abstract

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.
Original languageEnglish
Pages (from-to)1319-1327
JournalRNA-A Publication of the RNA Society
Volume18
Issue number7
DOIs
Publication statusPublished - 2012

Keywords

  • multiple sequence alignment
  • in-vitro selection
  • base-pairs
  • aminoglycoside antibiotics
  • molecular discrimination
  • nucleotide composition
  • aptamer complex
  • binding rna
  • recognition
  • motifs

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    Widmann, J., Stombaugh, J., Mcdonald, D., Chocholousova, J., Gardner, P., Iyer, M. K., ... Knight, R. (2012). RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. RNA-A Publication of the RNA Society, 18(7), 1319-1327. https://doi.org/10.1261/rna.032052.111