Secondary Structure Databases

From Eterna Wiki

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.

Name Description
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 FRAgments search engine & dataBASE.


See also