  We study the effect of a finite proximity superconducting (SC) coherence
length in SN and SNS junctions consisting of a semiconducting topological
insulating wire whose ends are connected to either one or two s-wave
superconductors. We find that such systems behave exactly as SN and SNS
junctions made from a single wire for which some regions are sitting on top of
superconductors, the size of the topological SC region being determined by the
SC coherence length. We also analyze the effect of a non-perfect transmission
at the NS interface on the spatial extension of the Majorana fermions.
Moreover, we study the effects of continuous phase gradients in both an open
and closed (ring) SNS junction. We find that such phase gradients play an
important role in the spatial localization of the Majorana fermions.
