The method described in this chapter can be used to infer putative functional 
links between two proteins. The basic idea is based on the principle of "guilt 
by association." It is assumed that two proteins, which are found to be 
transcribed by a single transcript in one (or several) genomes are likely to be 
functionally linked, for example by acting in a same metabolic pathway or by 
forming a multiprotein complex. This method is of particular interest for 
studying genes that exhibit no, or only remote, homologies with already 
well-characterized proteins. Combined with other non-homology based methods, 
gene fusion events may yield valuable information for hypothesis building on 
protein function, and may guide experimental characterization of the target 
protein, for example by suggesting potential ligands or binding partners. This 
chapter uses the FusionDB database (http://www.igs.cnrs-mrs.fr/FusionDB/) as 
source of information. FusionDB provides a characterization of a large number of 
gene fusion events at hand of multiple sequence alignments. Orthologous genes 
are included to yield a comprehensive view of the structure of a gene fusion 
event. Phylogenetic tree reconstruction is provided to evaluate the history of a 
gene fusion event, and three-dimensional protein structure information is used, 
where available, to further characterize the nature of the gene fusion. For 
genes that are not comprised in FusionDB, some instructions are given as how to 
generate a similar type of information, based solely on publicly available web 
tools that are listed here.