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

The complete list of viral species able to infect humans was retrieved from http://viralzone.expasy.org/all_by_species/678.html (accessed in April 2016) and, for each of them, all available complete genome sequences were downloaded from GenBank. Multiple alignments were built for each virus with usearch8 (Edgar 2010), using a permissive identity threshold (60%) to account for viral variability. Since in some cases nucleotide heterogeneity within viral species exceeded this value, multiple clusters of aligned sequences were obtained for some viruses, representing distinct genotypes. Considering the difficulty of obtaining high quality alignments beyond this limit of nucleotide similarity, all clusters obtained with this method were kept separate, manually assigned to specific genotypes and independently processed in the downstream analyses. One genome per each group of aligned sequences was chosen to serve as reference sequence, possibly belonging to the manually curated RefSeq database [https://www.ncbi.nlm.nih.gov/refseq/]. The complete list of selected reference sequences is reported in Supplemental_Material.pdf (Table S1 ).