# Dot-Bracket Notation

From EteRNA WiKi

Revision as of 19:03, 16 April 2013 by ElNando888 (Talk | contribs)

Dot-bracket notation is a convenient way of representing secondary structure. Each character represents a base. Open parentheses indicate that the base is paired to another base ahead of it. Closed parentheses indicate that a base is paired to another base behind it. Periods, or dots, indicate an unpaired base. The number of open and closed parentheses will always be equal. Some secondary structure databases include other characters ( [] , {}, <>, a, etc...) to represent pairing in pseudoknots. To convert these structures to the simple dot-bracket notation used in EteRNA, substitute a period for all of the alternate symbols.