Skip to main content
Figure 1 | BMC Genomics

Figure 1

From: GAP-Seq: a method for identification of DNA palindromes

Figure 1

High-throughput next generation sequencing of fast annealing DNA treated by S1 nuclease. (A) Sequencing library construction. We prepared samples for sequencing based on efficient intrastrand base pairing of palindromes. Briefly, the genomic DNA was denatured and rapidly reannealed. After single-strand specific S1 nuclease digestion, DNA was extracted by phenol-chloroform and libraries were prepared for 454 and Illumina sequencing. (B) Data analysis. 1: Mapping of unique reads to human reference genome (NCBI36/hg18). Black lines represent mapped unique reads. Hatched rectangles represent regions masked by RepeatMasker (M). 2: Assembly of uniquely mapped reads to identify contiguous regions (contigs, black rectangles), and calculation of base read ratio (B) of each contig. For a contig region “c” with n mapped reads, B c = r = 1 n c ReadLength r , c / ContigLength c . 3: Clustering two or more contigs with a base read ratio >1.5 that are within 7.5 kb of each other to make a joined contig. 4: Determining Rank “R” that is the sum of all read lengths in the joined contig divided by the length of the joined contig minus the masked regions R a = r = 1 n c ReadLength r , c / JoinedContigLength c M a .

Back to article page