Summary
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.
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Acknowledgments
Much of this research took place while the author was at the Laboratoire Génome et Informatique. At this time, implementation and data were publicly available on the Infobiogen website http://lgi.infobiogen.fr/DomainTeam whose team provided a substantial help for this. The author is grateful to the members of her present lab, Laboratoire Statistique et Génome, particularly to Mark Hoebeke who performed the migration of the website to http://stat.genopole.cnrs.fr/domainteams.
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Pasek, S. (2007). Domain Team. In: Bergman, N.H. (eds) Comparative Genomics. Methods In Molecular Biology™, vol 396. Humana Press. https://doi.org/10.1007/978-1-59745-515-2_2
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DOI: https://doi.org/10.1007/978-1-59745-515-2_2
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