antaRNA - Structure/Sequence Constraint Dependent Terrain Modification

The input of antaRNA can be modelled, such that structural and sequence constraints
can be made. The induced structure constraintand the hard sequence constraint are
managed wihtin the terrain:

Hard Sequence Constraint

The hard sequence constraint has immediate impact of the setup of the terrain.
Vertices and affiliated edges vare removed from the terrain, if specific nucleotides
or nucleotide sets are invoking constraint information. In the following example,
sequence position i is constrained by a guanine 'G', which imlies that all concurrent
vertices and their connecting edges are object of removal:

As for the standard IUPAC RNA nucleotides, the IUPAC RNA ambigious nucleotides
are processed in the same way.. Dependent of the respective constrained character,
all not fitting character vertices are removed from the terrain in order to
prevent usage within the algorithm.

Induced Structure Constraint

Dependend on the option 'inducing level', (0: no; 1: A, C, G, U; 2: T, R, Y, S, W, K, M; 3: B, D, H, V),
antaRNA is allowed to induce structure constraint from existing situations in order
to supplement the constraint decision of the user.

The inducing only works, if a terrain position is constrained by both, structure
and nucleotide of respcetive inducing level definition. Furthermore, the corresponding
position wihtin the terrain (base pair open or close) must be of complementary sequence
constraint character in order to further prune the terrain:

in the example position i and j should basepair. i is constrained by 'G', j by 'N'.
'G' and 'N' are compatible, with an inducing level of 1 (standard), corresponding
vertices and edges at position j are removed.

In the second example position i and j should basepair. i is constrained by 'S',
j by 'K'. 'S' and 'K' are partially compatible, with an inducing level of 2,
corresponding vertices and edges at position j are removed.

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Robert Kleinkauf 05/2015