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:
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 <ivo@tbi.univie.ac.at>
Last modified: 2003-02-14 16:18:17 ivo