====== 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 ([[g4virus#Data Download|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.
[[g4virus#Scripts and Supplementary files|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. ===== Search virus by name =====

Virus name:

===== Search virus by class ===== ==== Class 1: dsDNA (double-stranded DNA viruses) ==== * [[:g4virus:bk_polyomavirus|BK polyomavirus]] * [[:g4virus:cercopithecine_herpesvirus_type_1|Cercopithecine herpesvirus type 1]] * [[:g4virus:cercopithecine_herpesvirus_type_2|Cercopithecine herpesvirus type 2]] * [[:g4virus:cercopithecine_herpesvirus_type_5|Cercopithecine herpesvirus type 5]] * [[:g4virus:cercopithecine_herpesvirus_type_8|Cercopithecine herpesvirus type 8]] * [[:g4virus:cercopithecine_herpesvirus_type_9|Cercopithecine herpesvirus type 9]] * [[:g4virus:cercopithecine_herpesvirus_type_16|Cercopithecine herpesvirus type 16]] * [[:g4virus:cowpox_virus|Cowpox virus]] * [[:g4virus:epstein_barr_virus|Epstein Barr virus (Human herpesvirus 4)]] * [[:g4virus:human_adenovirus_a|Human adenovirus A]] * [[:g4virus:human_adenovirus_b|Human adenovirus B]] * [[:g4virus:human_adenovirus_c|Human adenovirus C]] * [[:g4virus:human_adenovirus_d|Human adenovirus D]] * [[:g4virus:human_adenovirus_e|Human adenovirus E]] * [[:g4virus:human_adenovirus_f|Human adenovirus F]] * [[:g4virus:human_adenovirus_g|Human adenovirus G]] * [[:g4virus:human_cytomegalovirus|Human cytomegalovirus (Human herpesvirus 5)]] * [[:g4virus:human_herpesvirus_1|Herpes simplex virus 1 (Human herpesvirus 1)]] * [[:g4virus:human_herpesvirus_2|Herpes simplex virus 2 (Human herpesvirus 2)]] * [[:g4virus:human_herpesvirus_6a|Human herpesvirus 6A]] * [[:g4virus:human_herpesvirus_6b|Human herpesvirus 6B]] * [[:g4virus:human_herpesvirus_7|Human herpesvirus 7]] * [[:g4virus:human_herpesvirus_8|Kaposi’s sarcoma-associated herpes virus (Human herpesvirus 8)]] * [[:g4virus:human_papillomavirus_1|Human papillomavirus 1]] * [[:g4virus:human_papillomavirus_2|Human papillomavirus 2]] * [[:g4virus:human_papillomavirus_16|Human papillomavirus 16]] * [[:g4virus:human_papillomavirus_18|Human papillomavirus 18]] * [[:g4virus:jc_polyomavirus|JC polyomavirus]] * [[:g4virus:ki_polyomavirus|KI Polyomavirus]] * [[:g4virus:merkel_cell_polyomavirus|Merkel cell polyomavirus]] * [[:g4virus:molluscum_contagiosum_virus|Molluscum contagiosum virus]] * [[:g4virus:monkeypox_virus|Monkeypox virus]] * [[:g4virus:orf_virus|Orf virus]] * [[:g4virus:vaccinia_virus|Vaccinia virus]] * [[:g4virus:varicella_zoster_virus|Varicella zoster virus (Human herpesvirus 3)]] * [[:g4virus:variola_virus|Variola virus]] * [[:g4virus:wu_polyomavirus|WU polyomavirus]] * [[:g4virus:yaba_like_disease_virus|Yaba like disease virus]] * [[:g4virus:yaba_monkey_tumor_virus|Yaba monkey tumor virus]] ==== Class 2: ssDNA (single-stranded DNA viruses) ==== * [[:g4virus:adeno_associated_virus|Adeno associated virus]] * [[:g4virus:human_bocavirus_2|Human bocavirus 2]] * [[:g4virus:human_parvovirus_b19|Human parvovirus B19]] * [[:g4virus:torque_teno_virus_1|Torque teno virus 1]] * [[:g4virus:torque_teno_virus_3|Torque teno virus 3]] * [[:g4virus:torque_teno_virus_4|Torque teno virus 4]] * [[:g4virus:torque_teno_virus_5|Torque teno virus 5]] * [[:g4virus:torque_teno_virus_sle|Torque teno virus SLE]] ==== Class 3: dsRNA (double-stranded RNA viruses) ==== * [[:g4virus:banna_virus_segment_1|Banna virus segment 1]] * [[:g4virus:banna_virus_segment_2|Banna virus segment 2]] * [[:g4virus:banna_virus_segment_3|Banna virus segment 3]] * [[:g4virus:banna_virus_segment_4|Banna virus segment 4]] * [[:g4virus:banna_virus_segment_5|Banna virus segment 5]] * [[:g4virus:banna_virus_segment_6|Banna virus segment 6]] * [[:g4virus:banna_virus_segment_7|Banna virus segment 7]] * [[:g4virus:banna_virus_segment_8|Banna virus segment 8]] * [[:g4virus:banna_virus_segment_9|Banna virus segment 9]] * [[:g4virus:banna_virus_segment_10|Banna virus segment 10]] * [[:g4virus:banna_virus_segment_11|Banna virus segment 11]] * [[:g4virus:banna_virus_segment_12|Banna virus segment 12]] * [[:g4virus:rotavirus_a_segment_1|Rotavirus A segment 1]] * [[:g4virus:rotavirus_a_segment_2|Rotavirus A segment 2]] * [[:g4virus:rotavirus_a_segment_3|Rotavirus A segment 3]] * [[:g4virus:rotavirus_a_segment_4|Rotavirus A segment 4]] * [[:g4virus:rotavirus_a_segment_5|Rotavirus A segment 5]] * [[:g4virus:rotavirus_a_segment_6|Rotavirus A segment 6]] * [[:g4virus:rotavirus_a_segment_7|Rotavirus A segment 7]] * [[:g4virus:rotavirus_a_segment_8|Rotavirus A segment 8]] * [[:g4virus:rotavirus_a_segment_9|Rotavirus A segment 9]] * [[:g4virus:rotavirus_a_segment_10|Rotavirus A segment 10]] * [[:g4virus:rotavirus_a_segment_11|Rotavirus A segment 11]] * [[:g4virus:rotavirus_b_segment_1|Rotavirus B segment 1]] * [[:g4virus:rotavirus_b_segment_2|Rotavirus B segment 2]] * [[:g4virus:rotavirus_b_segment_3|Rotavirus B segment 3]] * [[:g4virus:rotavirus_b_segment_4|Rotavirus B segment 4]] * [[:g4virus:rotavirus_b_segment_5|Rotavirus B segment 5]] * [[:g4virus:rotavirus_b_segment_6|Rotavirus B segment 6]] * [[:g4virus:rotavirus_b_segment_7|Rotavirus B segment 7]] * [[:g4virus:rotavirus_b_segment_8|Rotavirus B segment 8]] * [[:g4virus:rotavirus_b_segment_9|Rotavirus B segment 9]] * [[:g4virus:rotavirus_b_segment_10|Rotavirus B segment 10]] * [[:g4virus:rotavirus_b_segment_11|Rotavirus B segment 11]] * [[:g4virus:rotavirus_c_segment_1|Rotavirus C segment 1]] * [[:g4virus:rotavirus_c_segment_2|Rotavirus C segment 2]] * [[:g4virus:rotavirus_c_segment_3|Rotavirus C segment 3]] * [[:g4virus:rotavirus_c_segment_4|Rotavirus C segment 4]] * [[:g4virus:rotavirus_c_segment_5|Rotavirus C segment 5]] * [[:g4virus:rotavirus_c_segment_6|Rotavirus C segment 6]] * [[:g4virus:rotavirus_c_segment_7|Rotavirus C segment 7]] * [[:g4virus:rotavirus_c_segment_8|Rotavirus C segment 8]] * [[:g4virus:rotavirus_c_segment_9|Rotavirus C segment 9]] * [[:g4virus:rotavirus_c_segment_10|Rotavirus C segment 10]] * [[:g4virus:rotavirus_c_segment_11|Rotavirus C segment 11]] ==== Class 4: (+)ssRNA (positive-sense single-stranded RNA viruses) ==== * [[:g4virus:aichi_virus|Aichi virus]] * [[:g4virus:barmah_forest_virus|Barmah forest virus]] * [[:g4virus:chikungunya_virus|Chikungunya virus]] * [[:g4virus:cosavirus_a|Cosavirus A]] * [[:g4virus:coxsackievirus_a|Coxsackievirus A]] * [[:g4virus:coxsackievirus_b|Coxsackievirus B]] * [[:g4virus:dengue_virus_1|Dengue virus 1]] * [[:g4virus:dengue_virus_2|Dengue virus 2]] * [[:g4virus:dengue_virus_3|Dengue virus 3]] * [[:g4virus:dengue_virus_4|Dengue virus 4]] * [[:g4virus:eastern_equine_encephalitis_virus|Eastern equine encephalitis virus]] * [[:g4virus:echovirus|Enteric Cytopathic Human Orphan virus]] * [[:g4virus:encephalomyocarditis_virus|Encephalomyocarditis virus]] * [[:g4virus:enterovirus_d|Enterovirus D]] * [[:g4virus:gb_virus_c_hepatitis_g_virus|GB virus C]] * [[:g4virus:hepatitis_c_virus_genotype_1|Hepatitis C virus genotype 1]] * [[:g4virus:hepatitis_c_virus_genotype_2|Hepatitis C virus genotype 2]] * [[:g4virus:hepatitis_c_virus_genotype_3|Hepatitis C virus genotype 3]] * [[:g4virus:hepatitis_c_virus_genotype_4|Hepatitis C virus genotype 4]] * [[:g4virus:hepatitis_c_virus_genotype_5|Hepatitis C virus genotype 5]] * [[:g4virus:hepatitis_c_virus_genotype_6|Hepatitis C virus genotype 6]] * [[:g4virus:hepatitis_e_virus|Hepatitis E virus]] * [[:g4virus:human_astrovirus|Human astrovirus]] * [[:g4virus:human_coronavirus_hcov_229e|Human coronavirus HCoV 229E]] * [[:g4virus:human_coronavirus_hcov_oc43|Human coronavirus HCoV OC43]] * [[:g4virus:human_coronavirus_hcov_hku1|Human coronavirus HCoV HKU1]] * [[:g4virus:human_coronavirus_hcov_nl63|Human coronavirus HCoV NL63]] * [[:g4virus:human_enterovirus_c|Enterovirus C]] * [[:g4virus:human_hepatitis_a_virus|Hepatitis A virus]] * [[:g4virus:human_poliovirus_1|Poliovirus 1]] * [[:g4virus:human_rhinovirus_a|Rhinovirus A]] * [[:g4virus:human_rhinovirus_b|Rhinovirus B]] * [[:g4virus:human_rhinovirus_c|Rhinovirus C]] * [[:g4virus:human_rhinovirus_d|Rhinovirus D]] * [[:g4virus:human_sars_coronavirus|SARS coronavirus]] * [[:g4virus:japanese_encephalitis_virus|Japanese encephalitis virus]] * [[:g4virus:langat_virus|Langat virus]] * [[:g4virus:lordsdale_virus|Lordsdale virus]] * [[:g4virus:louping_ill_virus|Louping ill virus]] * [[:g4virus:mayaro_virus|Mayaro virus]] * [[:g4virus:mers_coronavirus|MERS coronavirus]] * [[:g4virus:murray_valley_encephalitis_virus|Murray valley encephalitis virus]] * [[:g4virus:norovirus_gi|Norovirus GI]] * [[:g4virus:onyong_nyong|O’nyong’nyong virus]] * [[:g4virus:porcine_enteric_sapovirus|Porcine enteric sapovirus]] * [[:g4virus:powassan_virus|Powassan virus]] * [[:g4virus:rosavirus_2|Rosavirus 2]] * [[:g4virus:ross_river_virus|Ross river virus]] * [[:g4virus:rubella_virus|Rubella virus]] * [[:g4virus:sagiyama_virus|Sagiyama virus]] * [[:g4virus:salivirus_a|Salivirus A]] * [[:g4virus:sapovirus_c12|Sapovirus C12]] * [[:g4virus:sapovirus_hu_dresden_pjg_sapo01_de|Sapovirus hu dresden pjg sapo01 de]] * [[:g4virus:sapovirus_hu_nagoya_ngy_1_2012_jpn|Sapovirus hu nagoya ngy 1 2012 jpn]] * [[:g4virus:sapovirus_mc10|Sapovirus Mc10]] * [[:g4virus:semliki_forest_virus|Semliki forest virus]] * [[:g4virus:sindbis_virus|Sindbis virus]] * [[:g4virus:st_louis_encephalitis_virus|St louis encephalitis virus]] * [[:g4virus:venezuelan_equine_encephalitis_virus|Venezuelan equine encephalitis virus]] * [[:g4virus:western_equine_encephalitis_virus|Western equine encephalitis virus]] * [[:g4virus:west_nile_virus|West Nile virus]] * [[:g4virus:yellow_fever_virus|Yellow fever virus]] * [[:g4virus:zika_virus|Zika virus]] ==== Class 5: (-)ssRNA (negative-sense single-stranded RNA viruses) ==== * [[:g4virus:australian_bat_lyssavirus|Australian bat lyssavirus]] * [[:g4virus:bunyamwera_virus_segment_l|Bunyamwera virus segment L]] * [[:g4virus:bunyamwera_virus_segment_m|Bunyamwera virus segment M]] * [[:g4virus:bunyamwera_virus_segment_s|Bunyamwera virus segment S]] * [[:g4virus:bunyavirus_la_crosse_segment_l|La Crosse segment L]] * [[:g4virus:bunyavirus_la_crosse_segment_m|La Crosse segment M]] * [[:g4virus:bunyavirus_la_crosse_segment_s|La Crosse segment S]] * [[:g4virus:crimean_congo_hemorrhagic_fever_virus_segment_l|Crimean Congo hemorrhagic fever virus segment L]] * [[:g4virus:crimean_congo_hemorrhagic_fever_virus_segment_m|Crimean Congo hemorrhagic fever virus segment M]] * [[:g4virus:crimean_congo_hemorrhagic_fever_virus_segment_s|Crimean Congo hemorrhagic fever virus segment S]] * [[:g4virus:dugbe_virus_segment_l|Dugbe virus segment L]] * [[:g4virus:dugbe_virus_segment_m|Dugbe virus segment M]] * [[:g4virus:dugbe_virus_segment_s|Dugbe virus segment S]] * [[:g4virus:ebolavirus|Ebolavirus]] * [[:g4virus:european_bat_lyssavirus|European bat lyssavirus]] * [[:g4virus:hantaan_virus_segment_l|Hantaan virus segment L]] * [[:g4virus:hantaan_virus_segment_m|Hantaan virus segment M]] * [[:g4virus:hantaan_virus_segment_s|Hantaan virus segment S]] * [[:g4virus:hendra_virus|Hendra virus]] * [[:g4virus:hepatitis_delta_virus|Hepatitis delta virus]] * [[:g4virus:human_parainfluenza_virus_1|Human parainfluenza virus 1]] * [[:g4virus:human_parainfluenza_virus_2|Human parainfluenza virus 2]] * [[:g4virus:human_parainfluenza_virus_3|Human parainfluenza virus 3]] * [[:g4virus:human_parainfluenza_virus_4|Human parainfluenza virus 4]] * [[:g4virus:human_respiratory_syncytial_virus_rsva|Human respiratory syncytial virus A]] * [[:g4virus:human_respiratory_syncytial_virus_rsvb|Human respiratory syncytial virus B]] * [[:g4virus:influenza_a_virus_segment_1|Influenza A virus segment 1]] * [[:g4virus:influenza_a_virus_segment_2|Influenza A virus segment 2]] * [[:g4virus:influenza_a_virus_segment_3|Influenza A virus segment 3]] * [[:g4virus:influenza_a_virus_segment_4|Influenza A virus segment 4]] * [[:g4virus:influenza_a_virus_segment_5|Influenza A virus segment 5]] * [[:g4virus:influenza_a_virus_segment_6|Influenza A virus segment 6]] * [[:g4virus:influenza_a_virus_segment_7|Influenza A virus segment 7]] * [[:g4virus:influenza_a_virus_segment_8|Influenza A virus segment 8]] * [[:g4virus:influenza_b_virus_segment_1|Influenza B virus segment 1]] * [[:g4virus:influenza_b_virus_segment_2|Influenza B virus segment 2]] * [[:g4virus:influenza_b_virus_segment_3|Influenza B virus segment 3]] * [[:g4virus:influenza_b_virus_segment_4|Influenza B virus segment 4]] * [[:g4virus:influenza_b_virus_segment_5|Influenza B virus segment 5]] * [[:g4virus:influenza_b_virus_segment_6|Influenza B virus segment 6]] * [[:g4virus:influenza_b_virus_segment_7|Influenza B virus segment 7]] * [[:g4virus:influenza_b_virus_segment_8|Influenza B virus segment 8]] * [[:g4virus:influenza_c_virus_segment_1|Influenza C virus segment 1]] * [[:g4virus:influenza_c_virus_segment_2|Influenza C virus segment 2]] * [[:g4virus:influenza_c_virus_segment_3|Influenza C virus segment 3]] * [[:g4virus:influenza_c_virus_segment_4|Influenza C virus segment 4]] * [[:g4virus:influenza_c_virus_segment_5|Influenza C virus segment 5]] * [[:g4virus:influenza_c_virus_segment_6|Influenza C virus segment 6]] * [[:g4virus:influenza_c_virus_segment_7|Influenza C virus segment 7]] * [[:g4virus:junin_arenavirus_segment_l|Junin virus segment L]] * [[:g4virus:junin_arenavirus_segment_s|Junin virus segment S]] * [[:g4virus:lake_victoria_marburgvirus|Lake Victoria marburgvirus]] * [[:g4virus:lassa_virus_segment_l|Lassa virus segment L]] * [[:g4virus:lassa_virus_segment_s|Lassa virus segment S]] * [[:g4virus:lymphocytic_choriomeningitis_virus_segment_l|Lymphocytic choriomeningitis virus segment L]] * [[:g4virus:lymphocytic_choriomeningitis_virus_segment_s|Lymphocytic choriomeningitis virus segment S]] * [[:g4virus:machupo_virus_segment_l|Machupo virus segment L]] * [[:g4virus:machupo_virus_segment_s|Machupo virus segment S]] * [[:g4virus:measles_virus|Measles virus]] * [[:g4virus:mokola_virus|Mokola virus]] * [[:g4virus:mumps_virus|Mumps virus]] * [[:g4virus:nipah_virus|Nipah virus]] * [[:g4virus:oropouche_virus_segment_l|Oropouche virus segment L]] * [[:g4virus:oropouche_virus_segment_m|Oropouche virus segment M]] * [[:g4virus:oropouche_virus_segment_s|Oropouche virus segment S]] * [[:g4virus:pichinde_virus_segment_l|Pichinde virus segment L]] * [[:g4virus:pichinde_virus_segment_s|Pichinde virus segment S]] * [[:g4virus:puumala_virus_segment_l|Puumala virus segment L]] * [[:g4virus:puumala_virus_segment_m|Puumala virus segment M]] * [[:g4virus:puumala_virus_segment_s|Puumala virus segment S]] * [[:g4virus:rabies_virus|Rabies virus]] * [[:g4virus:rift_valley_fever_virus_segment_l|Rift valley fever virus segment L]] * [[:g4virus:rift_valley_fever_virus_segment_m|Rift valley fever virus segment M]] * [[:g4virus:rift_valley_fever_virus_segment_s|Rift valley fever virus segment S]] * [[:g4virus:seoul_virus_segment_l|Seoul virus segment L]] * [[:g4virus:seoul_virus_segment_m|Seoul virus segment M]] * [[:g4virus:seoul_virus_segment_s|Seoul virus segment S]] * [[:g4virus:toscana_virus_segment_l|Toscana virus segment L]] * [[:g4virus:toscana_virus_segment_m|Toscana virus segment M]] * [[:g4virus:toscana_virus_segment_s|Toscana virus segment S]] * [[:g4virus:uukuniemi_virus_segment_l|Uukuniemi virus segment L]] * [[:g4virus:uukuniemi_virus_segment_m|Uukuniemi virus segment M]] * [[:g4virus:uukuniemi_virus_segment_s|Uukuniemi virus segment S]] * [[:g4virus:vesicular_stomatitis_virus_indiana|Vesicular stomatitis virus Indiana]] * [[:g4virus:vesicular_stomatitis_virus_new_jersey|Vesicular stomatitis virus New Jersey]] ==== Class 6: ssRNA-RT (positive-sense single-stranded RNA viruses that replicate through a DNA intermediate) ==== * [[:g4virus:hiv_1|Human immunodeficiency virus 1]] * [[:g4virus:htlv_1|Human T-lymphotropic virus 1]] * [[:g4virus:htlv_2|Human T-lymphotropic virus 2]] * [[:g4virus:human_spumaretrovirus|Human spumaretrovirus]] * [[:g4virus:simian_foamy_virus|Simian foamy virus]] * [[:g4virus:siv|Simian immunodeficiency virus]] * [[:g4virus:stlv1|Simian T-lymphotropic virus 1]] ==== Class 7: dsDNA-RT (double-stranded DNA viruses that replicate through a single-stranded RNA intermediate) ==== * [[:g4virus:hepatitis_b_virus|Hepatitis B virus]] ===== Data download ===== {{filelist>docs/g4virus/data_download/*&style=table&tableheader=1&tableshowdate=1&tableshowsize=1&direct=1&recursive=0}} - 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 ===== {{filelist>docs/g4virus/script_tables/*&style=table&tableheader=1&tableshowdate=1&tableshowsize=1&direct=1&recursive=0}} - 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.