The bracket notation for RNA secondary structures

Pseudo-knot free secondary structures can be represented in the space-efficient bracket notation, which is used throughout the Vienna RNA package. A structure on a sequence of length n is represented by a string of equal length consisting of matching brackets and dots. A base pair between base i and j is represented by a '(' at position i and a ')' at position j, unpaired bases are represented by dots. Thus the secondary structure
is equivalent to:
secondary structure graph
i.e. a stem-loop structure consisting of a an outer helix of 3 base pairs followed by an interior loop of size 3, a second helix of length 4, and a hairpin loop of size 3.

Base pair probabilities are sometimes summarized in pseudo bracket notation with the additional symbols ',', '|', '{', '}'. Here, the usual '(', ')', '.', represent bases with a strong preference (more than 2/3) to pair upstream (with a partner further 3'), pair down-stream, or not pair, respectively. '{', '}', and ',' are just weaker version of the above and '|' represents a base that is mostly paired but has pairing partners both upstream and downstream. In this case open and closed brackets need not match up.

Ivo Hofacker <>
Last modified: 2003-02-14 16:18:17 ivo