The presence of a conserved G-quadruplex (G4) pattern within a less conserved genome environment could be an indication of a G4 with a biological function. Here, we report in a graphical form the relationship between these two features calculated among the available strains. To allow for a fast evaluation of G4 conservation in the local genomic context, the “G4 scaffold conservation index” (G4_SCI) was computed. This value measures the degree of conservation of G-islands that are necessary and sufficient to form a G4: the higher the score, the higher the conservation of the G4 pattern. All G4s are plotted as vertical bars, whose height and position represent the G4_SCI on the y-axis and the genome coordinates on the x-axis, respectively. In addition, the local sequence conservation (LCS) of the viral genome, the sequence complexity and the sequence entropy are reported alongside.
note 1: the graphs are interactive. By clicking on the legend is possible to add and remove tracks, while hovering over the curves returns point values. It is also possible to zoom in by selecting a specific area of the graphs.
note 2: when more than four G-islands are found complying with the maximum distance allowed between consecutive islands, only one bar is plotted in the middle of the region. Nevertheless, multiple distinct G4s or isoforms could form.
note 3: further links are available on the top of each chart, redirecting to interactive pages for the visualization of G-quadruplexes in multiple alignments and annotated reference sequences. Please note that boundaries of G4 regions are determined by the multiple alignments and some of the islands might not be present in the reference genome itself. Consider this when visualizing the annotated reference.
The presence of G4 patterns may be largely affected by G/C content, which greatly varies in viral genomes. To check whether the presence of putative G4s is potentially relevant or whether it occurs by pure chance, different simulated datasets were generated for each virus as follows:
The presence of G4 was evaluated in all of these simulated sequences and the results were compared with those obtained from real data. The significance of the observed numbers of G4s with respect to real viral genomes is calculated with the mid-P value. The results are presented as segment diagrams, where each segment is referred to one of the three G-island types (GG, GGG, GGGG) considered in the positive and negative strands, while its length corresponds to 1 minus the mid-P value. Full segments indicate highly significant G4s, whereas null segments indicate non-significant G4s. The statistical significance is set to 0.1 (0.05 for each tail) and is shown as a grey area within the charts (slices that exceed this area are significant). The color indicates the tail of the distribution to which mid-P values are referred: green and red mean that G4s are enriched in real or in simulated sequences, respectively.