The PAUSE software has been developed as a new tool to study translational 
control over protein targeting. This makes it possible to correlate the position 
of clusters of rare codons in a gene, predicted to cause a translational pause, 
with the position of hydrophobic stretches in the encoded protein, predicted to 
span a membrane or to act as a cleavable signal for targeting to the secretory 
pathway. Furthermore, this software gathers these correlations over whole sets 
of genes. The PAUSE software is described here, and its use is illustrated on a 
set of membrane proteins from the fungus Emericella nidulans. Preferential 
distances of about 45 codons and of about 70 codons between putative 
transmembrane domains and predicted translational pauses were observed. Given 
that approximately 30 residues are required to span the large ribosomal subunit, 
the predicted pauses would therefore occur when the hydrophobic domain starts 
protruding from the ribosome ('+45 pause'), or fully protrudes as a hairpin 
('+70 pause'). Thus, these specific pauses might reflect a translational control 
over membrane protein targeting or early recognition ('+45 pause'), and over 
insertion or folding ('+70 pause').