BACKGROUND: It has recently been shown that the detection of gene fusion events 
across genomes can be used for predicting functional associations of proteins, 
including physical interaction or complex formation. To obtain such predictions 
we have made an exhaustive search for gene fusion events within 24 available 
completely sequenced genomes.
RESULTS: Each genome was used as a query against the remaining 23 complete 
genomes to detect gene fusion events. Using an improved, fully automatic 
protocol, a total of 7,224 single-domain proteins that are components of gene 
fusions in other genomes were detected, many of which were identified for the 
first time. The total number of predicted pairwise functional associations is 
39,730 for all genomes. Component pairs were identified by virtue of their 
similarity to 2,365 multidomain composite proteins. We also show for the first 
time that gene fusion is a complex evolutionary process with a number of 
contributory factors, including paralogy, genome size and phylogenetic distance. 
On average, 9% of genes in a given genome appear to code for single-domain, 
component proteins predicted to be functionally associated. These proteins are 
detected by an additional 4% of genes that code for fused, composite proteins.
CONCLUSIONS: These results provide an exhaustive set of functionally associated 
genes and also delineate the power of fusion analysis for the prediction of 
protein interactions.