Algorithmic Representation of Large RNA Folding Landscapes

Abstract

In evolutionary processes on the molecularlevel, neutral alterations play an important role [Kim83]. The primary sequence of a DNA or RNA moleculeis changed by errors introduced by the replication machinery at certain rates. Such a mutation does not necessarily affect the phenotype. The molecule’s contribution to the individual’s overall fitness is mediated by its function. For non-encoding RNA, the function in turn is determined by the 3D-structure of the molecule. A mutation in the primary sequence of such an RNA molecule that does notalter its structure is called neutral.