Abstract
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.