|
24h Post Lytic Activation (1/3) - BAM Coverage |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564919 |
SRR10564919 |
View on JBrowse |
|
24h Post Lytic Activation (2/3) - BAM Coverage |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564920 |
SRR10564920 |
View on JBrowse |
|
24h Post Lytic Activation (3/3) - BAM Coverage |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564921 |
SRR10564921 |
View on JBrowse |
|
3h Post Lytic Activation (1/3) - BAM Coverage |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564916 |
SRR10564916 |
View on JBrowse |
|
3h Post Lytic Activation (2/3) - BAM Coverage |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564917 |
SRR10564917 |
View on JBrowse |
|
3h Post Lytic Activation (3/3) - BAM Coverage |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564918 |
SRR10564918 |
View on JBrowse |
|
48h Post Lytic Activation (1/3) - BAM Coverage |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564922 |
SRR10564922 |
View on JBrowse |
|
48h Post Lytic Activation (2/3) - BAM Coverage |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564923 |
SRR10564923 |
View on JBrowse |
|
48h Post Lytic Activation (3/3) - BAM Coverage |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564924 |
SRR10564924 |
View on JBrowse |
|
All Chromosome - Full Data Set - Forward Strand Windows |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
|
All Chromosome - Full Data Set - Reverse Strand Windows |
Homo sapiens (Human) |
RNAStructuromeDB |
GRCh38 |
View on JBrowse |
|
ArcTest |
Homo sapiens (Human) |
Test |
Test |
View on JBrowse |
|
A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs. |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
ScanFold |
ScanFold |
|
|
BAM18 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564918 |
SRR10564918 |
View on JBrowse |
|
BAM19 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564919 |
SRR10564919 |
View on JBrowse |
|
BAM20 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564920 |
SRR10564920 |
View on JBrowse |
|
BAM21 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564921 |
SRR10564921 |
View on JBrowse |
|
BAM22 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564922 |
SRR10564922 |
View on JBrowse |
|
BAM23 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564923 |
SRR10564923 |
View on JBrowse |
|
BAM24 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
SRR10564924 |
SRR10564924 |
View on JBrowse |
|
BAM Test |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
bowtie 2 |
Nascent Transcriptomics Reveal Cellular Prolytic Factors Upregulated Upstream of the Latent-to-Lytic Switch Protein of Epstein-B |
View on JBrowse |
|
Clinical SNP Variants |
Homo sapiens (Human) |
NCBI ClinVar dataset |
NCBI |
View on JBrowse |
|
Conservation Score (from 100 vertebrates) |
Homo sapiens (Human) |
phastCons100way |
UCSC |
View on JBrowse |
|
DFAM Track |
Homo sapiens (Human) |
UCSC Genome Browser RepeatMasker |
USCS Genome Browser |
View on JBrowse |
|
EBV-1 GFF3 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
NCBI |
NC_007605.1 |
View on JBrowse |
|
EBV-2 GFF3 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 2 (EBV Type 2) |
NCBI |
NC_009334.1 |
View on JBrowse |
|
EBV Type 1 Forward Scan Results (GFF3) |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
ScanFold |
EBV Type 1 |
View on JBrowse |
|
Ensembl Annotations (release 91) |
Homo sapiens (Human) |
Ensembl Annotations |
Ensembl |
View on JBrowse |
|
Ensemble Diversity - GRCh38 - Forward Strand |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
|
Ensemble Diversity - GRCh38 - Reverse Strand |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
|
Ensemble Diversity Value |
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
ScanFold |
ScanFold |
View on JBrowse |
|
Ensemble Regulatory Build (Release 91) |
Homo sapiens (Human) |
Ensembl Regulatory Build |
homo_sapiens.GRCh38.Regulatory_Build.regulatory_features.20161111.gff.gz |
View on JBrowse |
|
Ensembl Variation (release 91) |
Homo sapiens (Human) |
Ensembl Variation |
ftp://ftp.ensembl.org/pub/release-91/variation/vcf/homo_sapiens/homo_sapiens.vcf.gz |
View on JBrowse |
|
Forward Arc Test EBV-1 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
ScanFold |
EBV Type 1 |
View on JBrowse |
|
Frequency of MFE - GRCh38 - Forward Strand |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
|
Frequency of MFE - GRCh38 - Reverse Strand |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
|
HCMV GFF3 |
Cytomegalovirus Human betaherpesvirus 5 (Human Cytomegalovirus) |
NCBI |
NC_006273.2 |
View on JBrowse |
|
Herpesvirus_Supplemental_Data_S1 |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
ScanFold |
ScanFold |
|
|
HHV-6A GFF3 |
Roseolovirus Human betaherpesvirus 6A (Human herpesvirus 6) |
NCBI |
NC_001664.4 |
View on JBrowse |
|
HHV-6B GFF3 |
Roseolovirus Human betaherpesvirus 6B (Human herpesvirus 6B) |
NCBI |
NC_000898.1 |
View on JBrowse |
|
HHV-7 GFF3 |
Roseolovirus Human betaherpesvirus 7 (Human Herpesvirus 7) |
NCBI |
NC_001716.2 |
View on JBrowse |
|
High Resolution Figures |
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
https://www.biorxiv.org/content/10.1101/2020.04.17.045161v1 |
SARS-CoV-2 |
|
|
HSV-1 GFF3 |
Simplexvirus Human alphaherpesvirus 1 (Herpes Simplex Virus 1) |
NCBI |
NC_001806.2 |
View on JBrowse |
|
HSV-2 GFF3 |
Simplexvirus Human alphaherpesvirus 2 (Herpes Simplex Virus 2) |
NCBI |
NC_001798.2 |
View on JBrowse |
|
KSHV GFF3 |
Rhadinovirus Human gammaherpesvirus 8 (Kaposi's sarcoma-associated herpesvirus) |
NCBI |
NC_009333.1 |
View on JBrowse |
|
LNCIPEDIA Hg38 Long Non-Coding RNA |
Homo sapiens (Human) |
LNCipedia |
LNCipedia.org |
View on JBrowse |
|
MFE |
Lentivirus Human immunodeficiency virus 1 (HIV-1) |
ScanFold-Scan |
ScanFold-Scan |
View on JBrowse |
|
MFE (kcal/mol) |
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
ScanFold |
ScanFold |
View on JBrowse |
|
Minimum Free Energy - GRCh38 - Forward Strand |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
|
Minimum Free Energy - GRCh38 - Reverse Strand |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
|
NCBI Genome Annotations |
Homo sapiens (Human) |
NCBI |
NCBI |
View on JBrowse |
|
p-value |
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
ScanFold |
ScanFold |
View on JBrowse |
|
P-Values - GRCh38 - Forward Strand |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
|
P-Values - GRCh38 - Reverse Strand |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
|
Rfam Bed Track (Version 13) |
Homo sapiens (Human) |
Manual annotations |
Rfam |
View on JBrowse |
|
RNACentral GFF3 Track |
Homo sapiens (Human) |
RNAcentral |
ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/releases/8.0/genome_coordinates/Homo_sapiens.GRCh38.gff.gz |
View on JBrowse |
|
RSV Gene Annotations |
Orthopneumovirus Human (Respiratory syncytial virus) |
ScanFold |
ScanFold |
View on JBrowse |
|
RSV(+strand; coding strand) MFE |
Orthopneumovirus Human (Respiratory syncytial virus) |
ScanFold |
ScanFold |
View on JBrowse |
|
RSV(+strand) Ensemble Diversity |
Orthopneumovirus Human (Respiratory syncytial virus) |
ScanFold |
ScanFold |
View on JBrowse |
|
RSV(-strand; genomic) MFE |
Orthopneumovirus Human (Respiratory syncytial virus) |
ScanFold |
ScanFold |
View on JBrowse |
|
RSV(+strand) ScanFold-Scan Results |
Orthopneumovirus Human (Respiratory syncytial virus) |
ScanFold |
ScanFold |
View on JBrowse |
|
RSV(-strand) z-score |
Orthopneumovirus Human (Respiratory syncytial virus) |
ScanFold |
ScanFold |
View on JBrowse |
|
RSV(+strand) z-score |
Orthopneumovirus Human (Respiratory syncytial virus) |
ScanFold |
ScanFold |
View on JBrowse |
|
SARS-CoV-2-ExtractedStructures |
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
ScanFold |
SARS-CoV-2 |
|
|
SARS-CoV-2 Gene Features |
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
NCBI |
NCBI |
View on JBrowse |
|
SARS-CoV-2 Results |
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
ScanFold |
SARS-CoV-2 |
|
|
Scanning Window Results (SARS-CoV-2) |
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
ScanFold |
SARS-CoV-2 |
View on JBrowse |
|
Supplemental Tables (10.1101/2020.04.17.045161) |
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
https://www.biorxiv.org/content/10.1101/2020.04.17.045161v1 |
https://www.biorxiv.org/content/10.1101/2020.04.17.045161v1 |
|
|
Thermodynamic z-score |
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
ScanFold |
ScanFold |
View on JBrowse |
|
VZV GFF3 |
Varicellovirus Human alphaherpesvirus 3 (Varicella-Zoster Virus) |
NCBI |
NC_001348.1 |
View on JBrowse |
|
ZIKV Features |
Flavivirus zika virus (Zika Virus) |
RNA Structurome DB |
NCBI NucCore |
View on JBrowse |
|
ZIKV MFE |
Flavivirus zika virus (Zika Virus) |
RNA Structurome DB |
RNA Structurome DB |
View on JBrowse |
|
ZIKV z-score |
Flavivirus zika virus (Zika Virus) |
RNA Structurome DB |
RNA Structurome DB |
View on JBrowse |
|
z-score |
Lentivirus Human immunodeficiency virus 1 (HIV-1) |
ScanFold-Scan |
ScanFold-Scan |
View on JBrowse |
|
Z-score Forward Strand (EBV-2) |
Lymphocryptovirus Human gammaherpesvirus 4 Type 2 (EBV Type 2) |
ScanFold |
EBV Type 2 |
View on JBrowse |
|
Z-score Forward Strand (EBV Type 1) |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
ScanFold |
EBV Type 1 |
View on JBrowse |
|
Z-score Forward Strand (HCMV) |
Cytomegalovirus Human betaherpesvirus 5 (Human Cytomegalovirus) |
ScanFold |
HCMV |
View on JBrowse |
|
Z-score Forward Strand (HHV-6A) |
Roseolovirus Human betaherpesvirus 6A (Human herpesvirus 6) |
ScanFold |
HHV-6A |
View on JBrowse |
|
Z-score Forward Strand (HHV-6B) |
Roseolovirus Human betaherpesvirus 6B (Human herpesvirus 6B) |
ScanFold |
HHV-6B |
View on JBrowse |
|
Z-score Forward Strand (HHV-7) |
Roseolovirus Human betaherpesvirus 7 (Human Herpesvirus 7) |
ScanFold |
ScanFold |
View on JBrowse |
|
Z-score Forward Strand (HSV-1) |
Simplexvirus Human alphaherpesvirus 1 (Herpes Simplex Virus 1) |
ScanFold |
ScanFold |
View on JBrowse |
|
Z-score Forward Strand (HSV-2) |
Simplexvirus Human alphaherpesvirus 2 (Herpes Simplex Virus 2) |
ScanFold |
ScanFold |
View on JBrowse |
|
Z-score Forward Strand (KSHV) |
Rhadinovirus Human gammaherpesvirus 8 (Kaposi's sarcoma-associated herpesvirus) |
ScanFold |
ScanFold |
View on JBrowse |
|
Z-score Forward Strand (VZV) |
Varicellovirus Human alphaherpesvirus 3 (Varicella-Zoster Virus) |
ScanFold |
ScanFold |
View on JBrowse |
|
Z-score Reverse Strand (EBV-2) |
Lymphocryptovirus Human gammaherpesvirus 4 Type 2 (EBV Type 2) |
ScanFold |
EBV-2 |
View on JBrowse |
|
Z-score Reverse Strand (EBV Type 1) |
Lymphocryptovirus Human gammaherpesvirus 4 Type 1 (EBV Type 1) |
ScanFold |
EBV Type 1 |
View on JBrowse |
|
Z-score Reverse Strand (HCMV) |
Cytomegalovirus Human betaherpesvirus 5 (Human Cytomegalovirus) |
ScanFold |
HCMV |
View on JBrowse |
|
Z-score Reverse Strand (HHV-6A) |
Roseolovirus Human betaherpesvirus 6A (Human herpesvirus 6) |
ScanFold |
HHV-6A |
View on JBrowse |
|
Z-score Reverse Strand (HHV-6B) |
Roseolovirus Human betaherpesvirus 6B (Human herpesvirus 6B) |
ScanFold |
HHV-6B |
View on JBrowse |
|
Z-score Reverse Strand (HHV-7) |
Roseolovirus Human betaherpesvirus 7 (Human Herpesvirus 7) |
ScanFold |
ScanFold |
View on JBrowse |
|
Z-score Reverse Strand (HSV-1) |
Simplexvirus Human alphaherpesvirus 1 (Herpes Simplex Virus 1) |
ScanFold |
ScanFold |
View on JBrowse |
|
Z-score Reverse Strand (HSV-2) |
Simplexvirus Human alphaherpesvirus 2 (Herpes Simplex Virus 2) |
ScanFold |
ScanFold |
View on JBrowse |
|
Z-score Reverse Strand (KSHV) |
Rhadinovirus Human gammaherpesvirus 8 (Kaposi's sarcoma-associated herpesvirus) |
ScanFold |
ScanFold |
View on JBrowse |
|
Z-score Reverse Strand (VZV) |
Varicellovirus Human alphaherpesvirus 3 (Varicella-Zoster Virus) |
ScanFold |
ScanFold |
View on JBrowse |
|
Z-Scores - GRCh38 - Forward Strand |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
|
Z-Scores - GRCh38 - Reverse Strand |
Homo sapiens (Human) |
RNAstructuromeDB |
GRCh38 |
View on JBrowse |
