We have previously shown that the detection of gene fusion events can contribute 
towards the elucidation of functional associations of proteins within entire 
genomes. Here we have analysed the entire genome of Drosophila melanogaster 
using fusion analysis and two additional constraints that improve the 
reliability of the predictions, viz. low sequence similarity and low degree of 
paralogy of the component proteins involved in a fusion event. Imposing these 
constraints, the total number of unique component pairs is reduced from 18 654 
to a mere 220 cases, which are expected to represent some of the most reliably 
detected functionally associated proteins. Using additional information from 
sequence databases, we have been able to detect pairs of functionally associated 
proteins with important functions in cellular and developmental pathways, such 
as spermatogenesis and programmed cell death.