Table 1.
Virus families.
Fig 1.
Example of virus classification in families, species and strains with data analysis flowchart.
The conservation analysis was performed among the strains within each virus species.
Fig 2.
Box and whisker plots of PQSs in different virus classes.
Each panel refers to the indicated type of G-island (GG, GGG, GGGG). The abundance of PQSs per 1 kb of viral genome is reported in the y-axis (for each viral species, the median value among all available strains is used) and the different virus categories in the x-axis. Boxplots are delimited by the first and third quartile and the straight and dotted lines drawn inside are the median and mean values, respectively, of the PQS distribution. The single observations are reported as dots close to the box plot. Whiskers delimit all the points that fall above/below the third/first quartile plus/minus 1.5 times the interquartile range (IQR). Orange and blue box plots refer to positive and negative strand respectively.
Fig 3.
Conservation of PQSs and viral genomes.
PQSs formed by GG-islands in the S segment of lymphocytic choriomeningitis virus are shown. PQSs found in the positive and negative strands are indicated as blue and orange vertical bars, respectively, while the height of bars represents the G4_SCI (the conservation of G-islands). Local sequence conservation (LSC) of viral genomes is shown as a red broken line. The x-axis indicates genome position, the y-axis the conservation %.
Table 2.
Relative abundance of viruses having a PQS content significantly different between real and simulated viral genomes.
Fig 4.
Different results from single nucleotide (SN) and islands (ISL) reshuffling strategies.
Heatmaps show all the viruses which are significant in only one of the two simulations or that obtain discordant results. Green and red boxes indicate that PQSs are more abundant in real and simulated genomes, respectively, with color intensity proportional to p-value size.
Table 3.
Confusion matrix for the semi-parametric classifier for G4 structure.