PMC

Schematic representation of subclusters, that is, clusters of conserved orthologous sequences that contain one region in each ortholog. See text for details. Rn, Rattus norvegicus; Mm, Mus musculus; Pt, Pan troglotydes; Hs, Homo sapiens.

Comparison of two-step strategy with MAVID for the scl data set (a) Conserved block: alignment of the different scl orthologs. The conserved block as identified by BlockSampler - is marked with a boxed area. (b) Visualization of the MAVID alignment of the corresponding region. The dashed line denotes a gap in the alignment. Rn, Rattus norvegicus; Mm, Mus musculus; Pt, Pan troglotydes; Hs, Homo sapiens; Fr, Fugu rubripes.

Schematic representation of the two-step procedure for phylogenetic footprinting. In the data reduction step, regions conserved among closely related (mammalian) orthologs are selected. Subsequently, these strongly conserved sequences are combined with a more distant ortholog (for example, Fugu); this set of genes is then subjected to motif detection. Finally, significantly conserved blocks are identified using a threshold defined by a random analysis.

Localization of clusters and conserved blocks in the (a) hoxb2, (b)pax6 and (c)scl datasets. For each dataset, the different orthologous intergenic sequences are shown: Rn,Rattus norvegicus; Mm, Mus musculus; Pt, Pan troglotydes; Hs, Homo sapiens; Fr, Fugu rubripes. Clusters of conserved mammalian subsequences that were subjected to motif detection (that is, clusters containing at least one subsequence per mammalian organism) are represented on the respective mammalian sequences (cluster 1 in red, cluster 2 in blue and cluster 3 in green). The conserved blocks identified using BlockSampler are represented on the Fugu intergenic sequence (in the color of the mammalian cluster it is located in). For each block the localization relative to the start of the Fugu gene is given. The transcription start sites are marked with an inverse triangle.