  Comparing strains within the same microbial species has proven effective in
the identification of genes and genomic regions responsible for virulence, as
well as in the diagnosis and treatment of infectious diseases. In this paper,
we present Sibelia, a tool for finding synteny blocks in multiple closely
related microbial genomes using iterative de Bruijn graphs. Unlike most other
tools, Sibelia can find synteny blocks that are repeated within genomes as well
as blocks shared by multiple genomes. It represents synteny blocks in a
hierarchy structure with multiple layers, each of which representing a
different granularity level. Sibelia has been designed to work efficiently with
a large number of microbial genomes; it finds synteny blocks in 31 S. aureus
genomes within 31 minutes and in 59 E.coli genomes within 107 minutes on a
standard desktop. Sibelia software is distributed under the GNU GPL v2 license
and is available at: https://github.com/bioinf/Sibelia Sibelia's web-server is
available at: http://etool.me/software/sibelia
