LoopModel

Nearest-neighbour model (Turner model) based on scoring loops closed by basepairs.

The implementation currently doesn't support:

• pseudoknots
• coaxial stacking
• multiple strands (although there is the scalar duplex_init)

Pairtable(dbn::String)

Compute the pair table (base pairs and strand extents) from dbn, a nucleic acid secondary structure given in dot-bracket notation.

In dot-bracket notation, unpaired bases are denoted by '.', base pairs are formed by pairing brackets '()[]{}<>', and strand ends (in a multi-strand complex) are indicated by '+'.

Throws an exception if the dot-bracket string is malformed (illegal characters or wrong number of opening or closing parentheses).

Examples

julia> Pairtable("(..)")
Pairtable([4, 0, 0, 1], StrandInfo[StrandInfo(1, 4, false)])

julia> Pairtable("(.(.[+.).].)")
Pairtable([11, 0, 7, 0, 9, 0, 3, 0, 5, 0, 1], StrandInfo[StrandInfo(1, 5, false), StrandInfo(6, 11, false)])

StrandInfo(startidx, endidx, iscircular)
StrandInfo(; startidx, endidx, iscircular)

Strand information used in a Pairtable: start index startidx of the strand in the Pairtable, end index endidx, and if the strand iscircular.

StrandInfo(startidx, endidx) = StrandInfo(startidx, endidx, false)

Strand information for a linear (non-circular) strand.

allseq(n::Integer; [bases])

Iterator over all sequences of length n. Optionally, the bases to be used can be specified.

allseq(pt::Pairtable; [bases], [basepairs])
allseq(dbn::String; [bases], [basepairs])

Iterator over all sequences compatible with a secondary structure given as a Pairtable pt or a string dbn in dot-bracket notation. Optionally, bases and basepairs to be used can be specified.

allstruct(seq::AbstractString; hpmin=3, canbp::Function=(s,i,j)->...)
allstruct(n::Integer; hpmin=3, canbp::Function)
allstruct(f::Function, seq::String; hpmin=3, canbp::Function)
allstruct(f::Function, n::Integer; hpmin=3, canbp::Function)

Iterate over all unpseudoknotted secondary structures, either for a given sequence seq or all structures of length n. The methods that take a function f as the first argument apply this function to every structure.

Optional arguments: minimum hairpin size is hpmin, and the function canbp specifies which bases can form basepairs.

filter_wildcard_chars(model::LoopModel)

Remove all parameters from tables that refer to wildcard nucleotides, e.g. 'N'.

numseq(pt::Pairtable; nbases=DEFAULT_NBASES, nbasepairs=DEFAULT_NBASEPAIRS)
numseq(dbn::String; nbases=DEFAULT_NBASES, nbasepairs=DEFAULT_NBASEPAIRS)

Number of sequences for a given secondary structure given as a Pairtable or as a string in dot-bracket notation. Optionally the number of possible bases nbases and basepairs nbasepairs can be specified.

numstruct(seq::AbstractString; hpmin=3)

Number of unpseudoknotted secondary structures for a sequence seq given as an AbstractString. The permissible base-pairs are Set([('U', 'A'), ('U', 'G'), ('G', 'U'), ('A', 'U'), ('C', 'G'), ('G', 'C')]), and additionally the base N can base-pair with any other base. The minimum allowed length of a hairpin loop is hpmin.

numstruct(n::Integer; hpmin=3)

Number of unpseudoknotted secondary structures for a sequence of length n. The minimum allowed length of a hairpin loop is hpmin. This function assumes that any base can base-pair with any other base.

randseq(n::Integer; [bases])

Random sequence of length n. Optionally, the possible bases to be used can be specified.

randseq(pt::Pairtable; [bases], [basepairs])
randseq(dbn::String; [bases], [basepairs])

Random sequence for a secondary structure given as a Pairtable or string in dot-bracket notation. Optionally, the bases and basepairs to be used can be specified.

readparam_viennarna(filepath; options...)

Read nearest-neighbour energy parameter file in ViennaRNA RNAfold v2.0 format.

Some implicit defaults for the ViennaRNA parameter file format:

• energy values are in units of 0.01 * kcal/mol
• parameters are assumed to be at 37 degrees Celsius

These can be configured with keyword arguments.

Note: for the intloop22 tables (named int22 and int22_enthalpies in the ViennaRNA parameter file), the tables are assumed to not consider bases or basepairs that contain an 'N'.