G4-virus: a comprehensive database for G-quadruplexes in human viruses

G4-virus: a comprehensive database for G-quadruplexes in human viruses

G-quadruplexes are non-canonical nucleic acid structures that control transcription, replication and translation, regulated genome recombination and genetic and epigenetic instability. G-quadruplexes are present in eukaryotes, prokaryotes and viruses. On this platform the analyses performed on all human viruses can be easily examined and downloaded.

Download

For each viral class of the Baltimore classification, a compressed tarball is available (here) and contains:

For each virus, multiple alignments comprehending all full genome sequences registered in GenBank (fasta format; we suggest to use Jalview for an easy visualization).
For each virus, the list of G-quadruplex coordinates and their conservation in the multiple alignment.
The list of G-quadruplex coordinates and their conservation with respect to a reference sequence selected for each virus (all the gaps present in the multiple alignments are removed in order to refer the coordinates to the original reference sequences).
One file with all “loop_conservation” values, calculated as the difference between G4_SCI (G4 scaffold conservation index) and LSC (local sequence conservation). See main text for further details.

Visualization

The list of all analyzed viruses in each class is provided. Viral names are links to dedicated pages containing visual information regarding G-quadruplexes found in each virus:

Conservation of G-quadruplexes and viral genomes.
Sequence complexity measures.
Statistical evidence for the calculated G4s in real virus genomes vs. randomized genomes (i.e. genomes with the same length and nucleotide composition, but not nucleotide order).
Further links for the visualization of G-quadruplexes in the multiple alignments and in the annotated reference sequence.

Supplementary files and scripts are available for download.

Publication

Lavezzo E, Berselli M, Frasson I, Perrone R, Palù G, Brazzale AR, Richter SN, Toppo S. (2018) G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide. PLoS Comput Biol 14(12): e1006675. https://doi.org/10.1371/journal.pcbi.1006675.

Hepatitis B virus

Data download

Filename	Filesize	Last modified
Reference_sequences.tar.gz	1.6 MiB	2018/08/01 16:38
dsDNA.tar.gz	37.7 MiB	2018/08/01 18:40
dsDNA_RT.tar.gz	2.7 MiB	2018/08/01 18:40
dsRNA.tar.gz	5.8 MiB	2018/08/01 18:40
ssDNA.tar.gz	125.6 KiB	2018/08/01 18:40
ssRNA_RT.tar.gz	32.6 MiB	2018/08/01 18:40
ssRNA_negative_polarity.tar.gz	12.8 MiB	2018/08/01 18:40
ssRNA_positive_polarity.tar.gz	14.5 MiB	2018/08/01 18:40

Reference_sequences.tar.gz: Fasta files of sequences used as references
dsDNA.tar.gz: Class 1, double-stranded DNA viruses
dsDNA_RT.tar.gz: Class 7, double-stranded DNA viruses that replicate through a single-stranded RNA intermediate
dsRNA.tar.gz: Class 3, double-stranded RNA viruses
ssDNA.tar.gz: Class 2, single-stranded DNA viruses
ssRNA_RT.tar.gz: Class 6, positive-sense single-stranded RNA viruses that replicate through a DNA intermediate
ssRNA_negative_polarity.tar.gz: Class 5, negative-sense single-stranded RNA viruses
ssRNA_positive_polarity.tar.gz: Class 4, positive-sense single-stranded RNA viruses

Scripts and supplementary files

Filename	Filesize	Last modified
Supplementary_Material.pdf	1019.6 KiB	2018/08/01 15:55
Supplementary_table_S3.xlsx	48.7 KiB	2018/08/01 15:55
scripts.tar.gz	204.2 KiB	2018/10/09 12:22

Supplementary_material.pdf: file containing all supplemental figures and tables cited in the paper.
Supplementary_table_S3.xlsx: list of viruses whose G4 content is significant at 10% with respect to randomized sequences.
scripts.tar.gz: scripts used to perform the analyses.

G4-virus: a comprehensive database for G-quadruplexes in human viruses

Download

Visualization

Publication

Search virus by name

Search virus by class

Class 1: dsDNA (double-stranded DNA viruses)

Class 2: ssDNA (single-stranded DNA viruses)

Class 3: dsRNA (double-stranded RNA viruses)

Class 4: (+)ssRNA (positive-sense single-stranded RNA viruses)

Class 5: (-)ssRNA (negative-sense single-stranded RNA viruses)

Class 6: ssRNA-RT (positive-sense single-stranded RNA viruses that replicate through a DNA intermediate)

Class 7: dsDNA-RT (double-stranded DNA viruses that replicate through a single-stranded RNA intermediate)

Data download

Scripts and supplementary files