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Figure 4 | BMC Genomics

Figure 4

From: Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis

Figure 4

EvoPrinterHD alignment scorecard. A) Once the eBLAT alignment phase is completed, the algorithm initially displays the data in a tabular/scorecard form. The total number of aligning bases for each pair-wise alignment (the homology score) is shown along with the position of the first and last aligning bases within the input reference DNA sequence. The genomes are arrayed in descending order of alignment score and the 3 highest pairwise alignment scores for each species are shown. The intra-genomic algorithm compares the second and third scoring alignments of each genome to its highest scoring alignment to identify potential regions that harbor conserved sequences that have either rearranged and/or duplicated, in addition to identifying sequencing gaps within the aligning regions. The input reference DNA eBLAT readouts and the aligning region BLAT for each alignment can be accessed by clicking on the species name and links to the Composite eBLATs are also provided. Each species can be selected or deselected for EvoPrinting and by default, EvoPrinterHD selects the 6 highest scoring species for generating the initial EvoPrint and EvoDifferences profile readouts. "Ns" represent the number of sequencing gaps detected in each of the aligning regions. The "R" value (indicative of a putative rearrangement) for the second and third alignments indicates the number of aligning bases not detected in the first alignment and the "D" value (indicative of a putative duplication) is the number of aligning bases shared with the first alignment. A link in provided for changing the input reference DNA to the aligning region of one of the other species. Shown is the alignment scorecard for a 3,570 bp Drosophila melanogaster sequence that is located 6 kb upstream of the fushi tarazu gene. As indicated by the "R/D" values for each of the species, the intra-genomic comparative program has identified potential rearrangements and duplications. The color code reveals 1) whether the R or D value is derived from the second or third alignment and 2) whether a putative rearrangement or duplication has been detected.

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