We describe a new method for reliably identifying conserved segments among genome sequences that have undergone rearrangement, horizontal transfer, and substantial nucleotide-level divergence. A Gibbs-like sampler explores different combinations of sequence-based markers shared by the genomes under study. The sampler assigns each marker a posterior probability based on how frequently it participates in some collinear group of markers. Markers with high p.p. values are likely members of conserved segments. The method identifies both large-scale and local trends in segmental collinearity, providing suitable input for genome alignment and rearrangement history inference tools. Applying our method to genomes of four
reveals that rearranged segments in these organisms belong in two size categories: large conserved segments that are interrupted by a staccato of single gene or operon-size small segments. The rearrangement pattern of large segments is best explained by symmetric inversions about the origin of replication while the pattern of small segments is not.
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