RNAStructML is a format for storing rna secondary structure information. One widely accepted usage for rnatools, such as RNAshapes {http://bibiserv.techfak.uni-bielefeld.de/rnashapes}, RNAfold {http://www.tbi.univie.ac.at/~ivo/RNA/} and Mfold {http://www.bioinfo.rpi.edu/applications/mfold/old/rna/form1.cgi} is the proprosal of rna secondary structures, based on thermodynamic principles. RNAStructML is based on SequenceML and uses Vienna style DotBracket strings for storing the structure information. element for storing RNA secondary structure information and some meta data optional version tag This contains the basic rna secondary structure data along with sequence information and program information data concerning programs and tools (e.g. commandline calls) can be stored in this element This contains the basic rna secondary structure data along with sequence information, but does not contain program information contains sequence information comment element This element is for storing rna secondary structure shapes. A shape defines a class of rna secondary structures. This element is for storing a specific rna secondary structure. A rna secondary structure may be related to a shape element. Type for storing sequence information. Inspired by SequenceML, but can not contain amino acid sequences name of the sequence synonyms for sequence name description for sequence this element can contain nucleotid sequences this element can contain unrestricted sequence strings this element is used if no sequence information is provided, it must be empty A comment can be placed in this element a mandatory sequence id Type for storing rna secondary structure shapes probability value for shape optional identifier for reference from structures Type for storing rna secondary structure information energy value for rna secondary structure probability value for rna secondary structure this attribute can contain a reference to a shape identifier simple type for probability attributes