Dot-Bracket Notation

From Eterna Wiki

Revision as of 16:31, 3 November 2013 by Omei (talk | contribs) (Removed the last sentence, which was incorrect.)

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.