<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>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 <italic>Drosophila melanogaster</italic> 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.</p>
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Comp Funct Genomics. 2003 Jun; 4(3):337-341