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Fig. 1 | BMC Genomics

Fig. 1

From: Genome-wide analysis of G-quadruplexes in herpesvirus genomes

Fig. 1

Genome-wide PQS densities and distribution of PQS. a Box plots showing average PQS densities (PQS/Kb) in full-length genomes of herpesviruses (HHV-1 to HHV-8; both strands for each virus). All available full-length sequences were analysed: HHV-1 (n = 8), HHV-2 (n = 3), HHV-3 (n = 52), HHV-4 (n = 5), HHV-5 (n = 47), HHV-6A (n = 3), HHV-6B (n = 1), HHV-7 (n = 2), HHV-8 (n = 5); please see Additional file 1 for accession numbers. The upper quartile in the box plot denotes the 75th percentile, the lower quartile denotes 25th percentile the upper and the lower bar denotes the maximum and minimum values and the central horizontal line denotes the median. b Schematic representation of the distribution of PQS in human herpesviruses. The genomes are drawn to scale. The black lines represent the two strands of the genomes. For each virus the upper black line represents the strand of DNA with 5′ to 3′ orientation (left to right) and the lower line represents the strand of DNA with 3′ to 5′ orientation (left to right). The red circles represent the genomic positions of PQS. The grey boxes represent the repeat regions in the genome. The total number of PQS present in a virus genome is shown in parentheses. Sequences used for creating the plot are HHV-1[Genbank:NC_001806], HHV-2[Genbank:NC_001798], HHV-3[Genbank:NC_001348], HHV-4 [Genbank:NC_007605], HHV-5[Genbank:NC_006273], HHV-6a[Genbank:NC_001664], HHV-6b[Genbank:NC_000898] HHV-7[Genbank:NC_001716] HHV-8[Genbank:NC_009333]. c Scatter plot showing correlation between GC% (x-axis) and PQS density (PQS/Kb) (y-axis) in herpesvirus genomes (P < 0.0001). d Native full length herpesvirus sequences (n = 126) are enriched for PQS compared to the randomized full length sequences (n = 630; five randomized sequences were analyzed for each native sequence). *denotes P < 0.001

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