MOTIVATION: Gene fusion is an important evolutionary process. It can yield 
valuable information to infer the interactions and functions of proteins. Fused 
genes have been identified as non-transitive patterns of similarity in triplets 
of genes. To be computationally tractable, this approach usually imposes an a 
priori distinction between a dataset in which fused genes are searched for, and 
a dataset that may have provided genetic material for fusion. This reduces the 
'genetic space' in which fusion can be discovered, as only a subset of triplets 
of genes is investigated. Moreover, this approach may have a high-false-positive 
rate, and it does not identify gene families descending from a common fusion 
event.
RESULTS: We represent similarities between sequences as a network. This leads to 
an efficient formulation of previous methods of fused gene identification, which 
we implemented in the Python program FusedTriplets. Furthermore, we propose a 
new characterization of families of fused genes, as clique minimal separators of 
the sequence similarity network. This well-studied graph topology provides a 
robust and fast method of detection, well suited for automatic analyses of big 
datasets. We implemented this method in the C++ program MosaicFinder, which 
additionally uses local alignments to discard false-positive candidates and 
indicates potential fusion points. The grouping into families will help 
distinguish sequencing or prediction errors from real biological fusions, and it 
will yield additional insight into the function and history of fused genes.
AVAILABILITY: FusedTriplets and MosaicFinder are published under the GPL license 
and are freely available with their source code at this address: 
http://sourceforge.net/projects/mosaicfinder.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics 
online.