G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide

Enrico Lavezzo; Michele Berselli; Ilaria Frasson; Rosalba Perrone; Giorgio Palù; Alessandra R. Brazzale; Sara N. Richter; Stefano Toppo

An example of the results from such analysis is reported in Figure 3 for both the lymphocytic choriomeningitis virus (segment S) and the human coxsackievirus A: all G4s for each virus are plotted as vertical bars, the height and position of which represent the G4_SCI on the yaxis and the genome coordinates on the x-axis, respectively. In addition, the local sequence conservation (LSC) of the viral genome, calculated with a sliding window approach on all available viral sequences and plotted as a red broken line, is reported alongside. This visualization method allows the prompt identification of the presence, position, and conservation of G-islands within G4s, together with the overall local conservation of the genomic context. Moreover, the degree of conservation of the connecting regions (loops) with respect to G-islands (the loop_conservation value) was calculated as the difference between G4_SCI and LSC. Positive and negative loop_conservation scores indicate, respectively, lower and higher conservation of connecting regions compared to the conservation of G-islands. Values close to zero mean that both G-islands and connecting author/funder. All rights reserved. No reuse allowed without permission.