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.
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Search |
Search for RNA STRAND entries, supports multiple search criteria |
Analyse
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Analyse one or a group of RNA secondary structures
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Submit
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Submit new RNA secondary structures to RNA STRAND |
News
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News and updates on new releases of the database |
Help
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Brief explanations of RNA STRAND input and output fields, also accessible via the '[?]' links on any RNA STRAND page |
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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.
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Structural feature occurences in RNA STRAND
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#RNAs |
#Occurences |
Structural motif |
2333 | 6746 |
Pseudoknots
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3582 | 17537 |
Multibranched
loops |
2992 | 35650 |
Internal
loops |
2898 | 31392 |
Bulge loops |
4575 | 43442 |
Hairpin
loops |
2296 | 48730 |
Non-canonical
base pairs |
Most common RNA types in RNA STRAND
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# 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 |
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Publication
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
Download
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.
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[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.
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[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.
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[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.]
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[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.
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[SprinzlDB] Sprinzl M, Vassilenko K: Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 2005, 33(Database issue):139-140.
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[RNasePDB] Brown J: The Ribonuclease P Database. Nucleic Acids Res 1999, 27:314-314.
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[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.
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[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.
Disclaimer
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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2004-2008 BETA LAB - University of British Columbia
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