Bioinformatics Group Freiburg

Institute of Computer Science
University Freiburg

antaRNA - GC Constraint Dependent Terrain Modification

The edges' GC specific information is initiallized according to the repsective
GC contraint which is defined by the user. The GC contraint dictates the respective
edge length. At this juncture, the length of an edge is determined according to
the nucleiotide fraction information of the target vertex, to which the specific
edge is leading to.

The 'AU' and the 'GC' nucleotide fractions are dealt in an opposing way,
such that, dependent on the currently requested GC content,the specific edge lenght
reflects the target GC specificly.


Since the ants prefer to walk short ways, the aim of this idea is to induce
a probability shift, such that a specified GC contraint is reached within the sequence.
So at an equilibrium state of 50%, poth, the 'AU' and the 'GC' edges share the
same length, since they have to be equally probable for the ants to pick.
No artificial path elongation is enforced. In the case of 25% targeted GC content,
the probabilities have to be shifted such that more 'AU' than 'GC' nucleotides are
incorporated into the sequence. This results in 'AU' edge lengths of 0.75 in contrast to 'GC'
edge lengths of 1.25.

Robert Kleinkauf 05/2015