The Genom of Homo sapiens.pdf

258 MARGULIES ET AL.Base Position 1,390,000 1,395,000 1,400,000 1,405,000CFTRX73053S64699DHS10aDHS10bConservationScoreMCSsChimpanzeeBaboon100%50%OrangutanMacaqueVervetLemurCatDogCowBlastz AlignmentsPigHorseRabbitHedgehogRatMousePlatypusOpossumDunnartChickenFuguTetraodonZebrafishFigure 3. UCSC Genome Browser view of multispecies sequences and their comparative analyses. Depicted is an adapted view ofthe UCSC Genome Browser (see http://genome.ucsc.edu) showing the data for a ~20-kb region within the CFTR gene (7q31.3 target;see Fig. 2), with sequence generated from 22 species. Along the top are shown standard UCSC Genome Browser tracks. The tracksthat are unique to the “zoo browser” are as follows: (1) Sites sensitive to cleavage by DNase I (DNase I hypersensitive sites DHS10aand DHS10b; Smith et al. 2000); (2) “Conservation Score,” which depicts the conservation score calculated at each position using themultispecies sequence data (see text and Fig. 4); (3) “MCSs,” which are regions exceeding an established conservation score thresholdthat together represent the top 5% most conserved sequence (Margulies et al. 2003); and (4) “Blastz Alignments,” which depictthe pair-wise alignments across the region between the indicated species’ sequence and the human reference sequence, with the y axisindicating the percent sequence identity (50–100%) within the alignments (if present). The small horizontal gray bar depicts a regionwhere there is currently no sequence for that species. Note that the vertical yellow lines, which are not present on the actual browser,highlight the positions of MCSs.