The human genome evolved over millions of years towards its current
form. Despite this long time its base composition did not reach a
stationary state yet. Instead one observes long range correlated
fluctuations of the Guanine-Cytosine (GC) content with an amplitude
about 10 times higher than expected. This so called isochore structure
of the genome is found in almost all warm-blooded vertebrates. The
origin, timing, and functional implications of this structure is
still controversial. We introduce a dynamical model, which could
explain the emergence of long-range correlations along chromosomes.
Further, we discuss consequences of long-range correlations to the
score statistics in sequence alignment as well as recent progress
to identify the underlying processes of the dynamical model in the
biological context.