Conservation properties in Fusarium promoters. (A) Phylogenetic relationship among four Fusarium species (unit of branch length is substitution per site). (B) Example of aligned sequences upstream of gene FGSG_11761 in Fg. The starred base positions are conserved across all four species. The sequence contains the candidate motif M3: ACGTCAT, discovered through our methods. (C) Excess conservation of heptamers in the promoter region of Fusarium species. The Motif Conservation Score (MCS) distribution indicates a bias towards excess conservation. The dashed curve is a hypothetical MCS distribution when the right and left sides are symmetric around zero. The excess conservation, outlying this dashed curve, is highlighted in red. The MCS value at the termination point of this dashed curve is used as the cut off to select the set of over-conserved heptamers.
Kumar et al. BMC Genomics 2010 11:208 doi:10.1186/1471-2164-11-208