We present here a method to identify microsyntenies across several genomes. This 
method adopts the innovative approach of deconstructing proteins into their 
domains. This allows the detection of strings of domains that are conserved in 
their content, but not necessarily in their order, that we refer to as domain 
teams or syntenies of domains. The prominent feature of the method is that it 
relaxes the rigidity of the orthology criterion and avoids many of the pitfalls 
of gene families identification methods, often hampered by multidomain proteins 
or low levels of sequence similarity. This approach, that allows both inter- and 
intrachromosomal comparisons, proves to be more sensitive than the classical 
methods based on pairwise sequence comparisons, particularly in the simultaneous 
treatment of many species. The automated and fast detection of domain teams is 
implemented in the DomainTeam software. In this chapter, we describe the 
procedure to run DomainTeam. After formatting the input and setting up the 
parameters, running the algorithm produces an output file comprising all the 
syntenies of domains shared by two or more (sometimes all) of the compared 
genomes.