Secondary Structure Databases
List of Secondary Structure Databases
If you want to design puzzles based on naturally-occurring RNAs, consider searching for a sequence in one of the online secondary structure databases listed below. You may have to break pseudoknots to create your puzzle (unless you choose a folding engine that supports pseudoknots, such as NUPACK). For structures represented in dot-bracket notation, this can be done by substituting a "." for symbols other than parentheses.
|RNA STRAND||Over 4000 secondary structures from a variety of sources. Structures available in dot-bracket notation.|
|Rfam||A collection of RNA families. Secondary structures must be saved through the VARNA applet.|
|RNA FRABASE 2.0
||RNA FRAgments search engine & dataBASE.