RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database

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RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database.
Current holdings: 4666 secondary structures in total.                                        
Search Search for RNA STRAND entries, supports multiple search criteria
Analyse one or a group of RNA secondary structures
Submit new RNA secondary structures to RNA STRAND
News and updates on new releases of the database
Brief explanations of RNA STRAND input and output fields, also accessible via the '[?]' links on any RNA STRAND page

Provenance of RNA STRAND structures
Source and link to source
1059RCSB Protein Data Bank
1056Gutell Lab CRW Site
726tmRNA Database
622Sprinzl tRNA Database
454RNase P Database
383SRP Database
313Rfam Database
53Nucleic Acid Database

Schematic representation of the secondary structure (a set of base pairs) for the RNase P RNA molecule of Methanococcus marapaludis from the RNase P Database; RNA STRAND ID is ASE_00199. Thick blue dots mark base pairs. Red dashed boxes mark structural features.
Structural feature occurences in RNA STRAND
#RNAs #Occurences Structural motif
23336746 Pseudoknots
358217537 Multibranched loops
299235650 Internal loops
289831392 Bulge loops
457543442 Hairpin loops
229648730 Non-canonical base pairs

Most common RNA types in RNA STRAND
# RNAs RNA type
726 Transfer Messenger RNA
723 16S Ribosomal RNA
707 Transfer RNA
470 Ribonuclease P RNA
450 Synthetic RNA
394 Signal Recognition Particle RNA
205 23S Ribosomal RNA
161 5S Ribosomal RNA
152 Group I Intron
146 Hammerhead Ribozyme
64 Other Ribosomal RNA
53 Other Ribozyme
42 Group II Intron
41 Cis-regulatory element


M. Andronescu, V. Bereg, H. H. Hoos, and A. Condon. RNA STRAND: The RNA Secondary Structure And Statistical Analysis Database. BMC Bioinformatics. 2008;9(1):340. [pubmed]

Supplementary material 1: List of Rfam published families which are included in RNA STRAND
Supplementary material 2: Description of the output of the RNA Secondary Structure Analyser


The RNA Secondary Structure Analyser
The RNA STRAND database

Conditions of use

We hope that you find RNA STRAND useful. If you use the database or analysis provided on this website in your research, we ask you to acknowledge this by citing the [STRAND] reference below. We thank the following sources for giving us permission to redistribute RNA sequence and secondary structure data: In addition, we ask you to acknowledge the original sources listed above of the RNA STRAND data that you use, and the corresponding publication listed below. Additional citations are available in the "Reference" field of each RNA STRAND entry page.
  • [STRAND] Andronescu M, Bereg V, Hoos HH, and Condon A: RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database. BMC Bioinformatics. 2008;9(1):340.
  • [PDB] Westbrook J, Feng Z, Chen L, Yang H, Berman H: The Protein Data Bank and structural genomics. Nucleic Acids Res 2003, 31:489-491.
  • [CRW] Cannone J, Subramanian S, Schnare M, Collett J, D'Souza L, Du Y, Feng B, Lin N, Madabusi L, Muller K, Pande N, Shang Z, Yu N, Gutell R: The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 2002, 3:2. [Correction: BMC Bioinformatics 3:15.]
  • [tmRDB,SRPDB] Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C: The tmRDB and SRPDB resources. Nucleic Acids Res 2006, 34(Database issue):163-168.
  • [SprinzlDB] Sprinzl M, Vassilenko K: Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 2005, 33(Database issue):139-140.
  • [RNasePDB] Brown J: The Ribonuclease P Database. Nucleic Acids Res 1999, 27:314-314.
  • [Rfam] Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy S, Bateman A: Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005, 33(Database issue):121-124.
  • [NDB] Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B: The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J 1992, 63(3):751-759.


Use of the RNA STRAND is free of charge. Although the authors have made every effort to ensure that the database and analyzer are correctly implemented, and fulfill the function described in the documentation, neither the authors nor the University of British Columbia guarantee its correctness, fitness for a particular purpose, or future availability.

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