Dot-Bracket Notation

A hairpin loop as it appears in EteRNA. Sequence and structure in dot-bracket notation appear below

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.