Figure 2

EvoPrints generated with e BLAT alignments reveal additional conserved sequences when compared to the original method. A) Shown is a composite EvoPrint of the Drosophila melanogaster Krüppel central domain (CD2) enhancer region generated by superimposing an EvoPrint generated from eBLAT alignments and a second prepared from BLAT alignments. Pairwise alignments between D. melanogaster and D. sechellia, D. simulans, D. erecta, D. yakuba, D. ananassae, D. pseudoobscura, D. persimilis, D. virilis, D. willistoni, D. mojavensis and D. grimshawi were used to generate both EvoPrints. Conserved sequences identified by both procedures are shown as uppercase black nucleotides and yellow highlighted nucleotides represent the additional sequences recognized by EvoPrinterHD. The boxed region contains the cis-regulatory DNA required for enhancer function as determined by Hoch et al. [9]. B) An EvoDifferences profile identifies those DNA sequences that are shared by all but one of the species included in the analysis. As in the EvoPrint, black uppercase letters indicate sequences shared by all species and colored uppercase letters, which denote individual species, represent sequences that were not detected by the eBLAT alignment for just one of the genomes included in the EvoPrint analysis (D. erecta, dark-red; D. yakuba, teal; D. pseudoobscura, light-blue; D. persimilis, brown; D. ananassae, pink; D. virilis, orange; D. willistoni, blue; D. mojavensis, green; or D. grimshawi, red). The underline indicates the region of the EvoDifferences profile that is compared with the alignments obtained from the UCSC genome browser (shown in panel C). C) Comparison of the EvoDifferences profile with the UCSC genome alignments. Shown is the underlined sequence in panel (B) aligned to the corresponding alignments obtained at the Drosophila UCSC comparative genome bioinformatics web site.