RNAStructAlignmentML is a format for storing rna secondary structure
alignments as computed by e.g. the RNAforester
{http://bibiserv.techfak.uni-bielefeld.de/rnaforester} or RNAalifold
{http://www.tbi.univie.ac.at/~ivo/RNA/} tool. RNAStructAlignment uses a
RNAStructML-like architecture, but uses AlignmentML instead of SequenceML as a basic
type.
this element contains rna secondary structure alignment information along with sequence and program information
optional version tag
this type can contain rna secondary structure alignment information along with sequence and program information
element for storing program/tool information e.g. command line calls
represents a rna structure alignment
element for storing sequence data. two sequences are required, since an alignment over one sequence does not make sense
this element can contain a comment
this element can contain consensus data for the alignment
score value
can contain identifier
type describing sequence data for rna secondary structure alignments. inspired by AlignmentML.
name of the sequence
synonyms for the name
sequence description
element for storing aligned nucleotid sequences
element for storing unrestricted aligned sequences
empty sequence element
element for storing rna secondary structure alignment belonging to the sequence
optional comment
mandatory sequence identifier
inherit gappedFreeSequenceType from hobitTypes; does not allow
gaps
An aligned nucleic acid sequence.
type for containing rna secondary structure alignments
energy value
probability value
type for containing rna secondary structure alignment consensus data
consensus rna secondary structure
structure probabilities
consensus sequence
optional identifier
type for consensus sequences
probability list describing consensus sequence probabilities
probability list describing consensus sequence probabilities
simple type for probabilities
Defines a list of structure probabilities, which is a triplet of two
positions and and a probability.
Defines a new type for structure probability. A structure probability
is defined by two bases and a pairing probability between them.
Position of the first base.
Position of the second base.
Probability of the base pair.