Statistics of Landscapes Based on Free Energies,
Replication and Degradation Rate Constants of RNA Secondary
Walter Fontana, Thomas Griesmacher, Wolfgang Schnabl,
Peter F Stadler, Peter Schuster
RNA secondary structures are computed from primary sequences by means
of a folding algorithm which uses a minimum free energy criterion.
Free energies as well as replication and degradation rate constants
are derived from secondary structures. These properties can be
understood as highly sophisticated functions of the individual
sequences whose values are mediated by the secondary structures. Such
functions induce complex value landscapes on the space of sequences.
The landscapes are analysed by random walk techniques, in particular
autocorrelation functions and correlation lengths are computed. Free
energy landscapes were found to be of AR(1) type. The rate constant
landscapes, however, turned out to be more complex. In addition,
gradient and adaptive walks are performed in order to get more insight
into the complex structure of the landscapes.
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