Prediction of Secondary Structures Conserved in Multiple RNA Sequences

Methods Mol Biol. 2016;1490:35-50. doi: 10.1007/978-1-4939-6433-8_3.


RNA structure is conserved by evolution to a greater extent than sequence. Predicting the conserved structure for multiple homologous sequences can be much more accurate than predicting the structure for a single sequence. RNAstructure is a software package that includes the programs Dynalign, Multilign, TurboFold, and PARTS for predicting conserved RNA secondary structure. This chapter provides protocols for using these programs.

Keywords: Comparative sequence analysis; RNA homology; RNA structure prediction.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Sequence
  • Computational Biology / methods
  • Conserved Sequence*
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • RNA / genetics
  • RNA, Ribosomal, 5S / chemistry
  • RNA, Ribosomal, 5S / genetics
  • Sequence Alignment
  • Software*
  • User-Computer Interface


  • RNA, Ribosomal, 5S
  • RNA