Author: Enrico Lavezzo; Michele Berselli; Ilaria Frasson; Rosalba Perrone; Giorgio Palù; Alessandra R. Brazzale; Sara N. Richter; Stefano Toppo
Title: G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide Document date: 2018_6_11
ID: c3lmmll6_49
Snippet: We evidenced some general trends and exceptions that are worth noting if seen in comparative terms among all viruses considered in this study. Starting from the general features we noted: i) high G/C content is not sufficient per se to generate a high number of G4s, as observed in G/C rich members of Herpesviridae family that are richer of putative G4s than expected. ii) The statistical significance of putative G4s found in real sequences tends t.....
Document: We evidenced some general trends and exceptions that are worth noting if seen in comparative terms among all viruses considered in this study. Starting from the general features we noted: i) high G/C content is not sufficient per se to generate a high number of G4s, as observed in G/C rich members of Herpesviridae family that are richer of putative G4s than expected. ii) The statistical significance of putative G4s found in real sequences tends to decrease when G-islands reshuffling (ISL) is compared with the corresponding single nucleotide assembling (SN), as is appreciable from the heatmap in Figure 4 (more intense color in the heatmap boxes). This suggests that short sequences of a given length (k-mer) could be over or underrepresented in certain viral genomes, as already reported in the literature (Greenbaum et al. 2008; Lobo et al. 2009 ). We observed that viral genomes enriched in putative G4s also contain a higher number of G-islands than expected from mere nucleotide composition, especially evident in the GG-islands. iii) The unevenly distribution of G4s can be used to classify membership of a virus in its corresponding category. This was author/funder. All rights reserved. No reuse allowed without permission.
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