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Incorporation of structure information

DCSE also allows easy incorporation of structure information within the alignment through the use of special symbols. The figure shows  two imaginary RNA sequences with these symbols, and drawings of the corresponding secondary structures. In the linear representation square brackets designate the beginning and end of one strand of a helix; a cirumflex separates adjacent helix strands. Braces are used to indicate beginning and end of bulges or internal loops, and a base taking part in a non-standard pair is enclosed in parentheses. The "Helix numbering" line identifies the helices.

Peter De Rijk