(((..((((...)))).)))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