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

To check whether the presence of putative G4s was statistically relevant or whether it occurred by pure chance, we compared the results obtained from real viral genomes with those obtained by two different simulation strategies. The first one (single nucleotide assembling) assumes that the occurrence of each DNA base in the genome is independent (Huppert and Balasubramanian 2005) ; the second (G-island reshuffling) considers that short sequences of a given length (k-mer) could be over or underrepresented in certain viral genomes (Greenbaum et al. 2008; Lobo et al. 2009 ). In the former case, sequences were generated with the same composition of nucleotides but different order with respect to references; in the latter, sequences were produced by reshuffling the positions of G-islands while keeping constant their number.