view genomes in gbrowse · 2020-04-20 · annotations of herpesviridae and poxviridae viruses...

11/2/12 1:45 PMHerpesviridae Annotations: 11.86 kbp from NC_001806:8,572..20,427

of 1http://www.vipr-dev.org/cgi-bin/gb2/gbrowse/herpes/?ref=NC_001806;start=1;stop=152261

Herpesviridae Annotations: 11.86 kbp from NC_001806:8,572..20,427

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Landmark or Region:NC_001806:8,572..20,427 Search

Examples: NC_001987, NC_001826:5000..10000, hypothetical protein.

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The Generic Genome Browser. For questions about the data at this site, please contact its webmaster. For support of the browser software only, sendemail to [email protected] or visit the GMOD Project web pages.

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Species: Human herpesvirus 1NCBI Protein ID: NP_044608Description: tegument protein UL7Location: 17135..18025View gene details in ViPR

Export the genome annotations/image with all features displayed in the GBrowse window in multiple formats

ViPR is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute and Vecna Technologies. Comments, questions, suggestions? Contact us at [email protected]

http://www.viprbrc.org/

Freely available Integrated datasets Bioinformatics tool suite

View Genomes in GBrowse

• Simultaneous bird's eye and detailed views of genomes and genome annotations of Herpesviridae and Poxviridae viruses

• Select and customize annotations using tracks • Upload and incorporate your own unpublished data into the genomic viewer

Adjust scale or click –/+ to zoom in/out

Check to flip the orientation to view minus strand genes

Displays the entire genome. The highlighted region is displayed in the Details panel and corresponds to the region you searched.

Displays a portion of the genome surrounding the region of interest

Pfam domain track: ViPR-generated Pfam domains

Hover over a feature to view its brief description; click to view its details in a new window.

Search genomic region by gene symbol, name, Accession number or coordinates

Gene track: Click to view gene/ protein details in a new window.

IEDB epitope track: Experimentally determined immune epitopes imported from IEDB

Click to show position

Click </> to scroll left/right

Click and drag the ruler to view base position

Displays the selected genome region corresponding to highlighted region in the Overview panel.

Click to configure the track

Release Date: Sep 7, 2012

This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between NorthropGrumman Health IT, J. Craig Venter Institute and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library, Wellcome Images, U.S. Department of Veterans Affairs ,Science of the Invisible and ViralZone, Swiss Institute of Bioinformatics.



Landmark or Region:NC_003401:61,937..65,236 SearchExamples: NC_001987, NC_001826:5000..10000, hypothetical protein.

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The Generic Genome Browser. For questions about the data at this site, please contact its webmaster. For support of the browser software only, send email [email protected] or visit the GMOD Project web pages.

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IEDB epitopes

Pfam domains

Pfam domains (0 bp..333.3 Mbp)(Currently showing 3.299 kbp)

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Herpesviridae

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Herpesviridae Annotations: 152.3 kbp from NC_001806:1..152,261

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Herpesviridae

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http://www.viprbrc.org/

Freely available Integrated datasets Bioinformatics tool suite

ViPR is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute and Vecna Technologies. Comments, questions, suggestions? Contact us at [email protected]

Access GBrowse GBrowse is available for Herpesviridae and Poxviridae viruses.

• On strain details page, look for “View in GBrowse” and follow the link; or • Click “View Genomes in GBrowse” from the “Analyze & Visualize” menu

to view a list of genomes viewable in GBrowse. Select a region

• Search a region using gene/protein symbol, name, accession number, or coordinates.

• Click and drag on a target genome region to select the region. Navigation

• Zoom in/out using the “Show XX bp” scale menu. • Change the zoom level by small increments using -/+. • Scroll left/right using <<, <, >, >> buttons. • Tick the “Flip” checkbox to flip the orientation such that the minus strand

points to the right. • Click and drag the ruler that shows base position.

Customize tracks – Each track corresponds to a type of genomic feature.

• Minimize a track by clicking ; turn off a track by clicking . • Reorder a track by clicking its name and dragging it up or down.

• Configure a track (display shape, height, color, etc.) by clicking . • Hover over a feature to view its brief description; click it to view its details

in a new window. • Download track data by using the “Download Track Data” menu. • Select tracks using the “Select Track” tab. • Upload a new annotation track: If you want to display additional

annotations on the genome, e.g., a region involved in virus reactivation, you can add your own tracks to the GBrowse window. Click the “Custom Tracks” tab. Then click “From text” in the “Add custom tracks” section. In the text box, type in coordinates and the feature name, one genomic feature per line, e.g., “NC_001806 10000 20000 reactivation” and click “Upload”. Click the “Browser” tab and you will see the uploaded track shown in the “Details” panel. You can also upload annotation files or import tracks from remote sources via the “Custom Tracks” tab.

Export

• Export the genome annotations/image with all features displayed in the GBrowse window in multiple formats (PNG image, GFF annotation table, or FASTA sequence file) by using the “Export as …” item accessible from the “File” drop-down menu.

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Protein Information (SOP)Gene Symbol Protein Product Name Entrez ID Locus Name Source

-N/A- Tegument protein UL51 -N/A- -N/A- GenBank

-N/A- DNA primase -N/A- -N/A- GenBank

-N/A- Glycoprotein K -N/A- -N/A- GenBank

GenBank Definition: Herpes simplex virus type 1 immediate-early protein Vmw68 geneand tandem repeat DNA, 5' end.

Authors: Murchie,M.J. and McGeoch,D.J.GenBank Sequence Accession: M24357Sequence Length: 457Sequence Status: Not CompleteSequence: View Nucleotide Sequence and design PCR primersNumber of Proteins: 1Organism Name: Human herpesvirus 1Mol Type: genomic DNA


GenBank Definition: Human herpesvirus 1, complete genome.

Authors:Dolan,A.,McGeoch,D.J., Dalrymple,M.A., Davison,A.J., Dolan,A.,Frame,M.C., McNab,D., Perry,L.J., Scott,J.E. andTaylor,P.,McGeoch,D.J.

GenBank Sequence Accession: NC_001806Sequence Annotations: View in GBrowseSequence Length: 152261Sequence Status: CompleteSequence: View Nucleotide Sequence and design PCR primersNumber of Proteins: 77Organism Name: Human herpesvirus 1Mol Type: genomic DNA

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Genome: M24357

Genome: NC_001806 Send Comments to Curator

Strain Name: 17Organism: Human herpesvirus 1

Taxonomy: Herpesviridae -> Alphaherpesvirinae -> Simplexvirus -> Humanherpesvirus 1

GenBank Host: Homo sapiensHost: HumanIsolation Country:

GenBank Definition: Human herpesvirus 1 isolate 17 glycoprotein G (US4) gene, partialcds.

Authors:Rekabdar,E., Tunback,P., Liljeqvist,J.A., Lindh,M. andBergstrom,T.,Rekabdar,E., Tunback,P., Liljeqvist,J.-A., Lindh,M. andBergstrom,T.

GenBank Sequence Accession: AF513130Sequence Length: 285Sequence Status: Not CompleteSequence: View Nucleotide Sequence and design PCR primersNumber of Proteins: 1Organism Name: Human herpesvirus 1Mol Type: genomic DNA


GenBank Definition: Human herpesvirus 5 isolate 17 UL143 gene, complete cds.Authors: He,R. and Ruan,Q.GenBank Sequence Accession: AY788102Sequence Length: 252Sequence Status: Not CompleteSequence: View Nucleotide Sequence and design PCR primersNumber of Proteins: 1Organism Name: Human herpesvirus 5Mol Type: genomic DNA


GenBank Definition: Human herpesvirus 5 isolate 17 UL144 gene, complete cds.

Authors: Mao,Z.Q., He,R., Sun,M., Qi,Y., Huang,Y.J. and Ruan,Q.,Mao,Z.Q.,Sun,M., Qi,Y., Ma,Y.P., He,R. and Ruan,Q.

GenBank Sequence Accession: AY818266Sequence Length: 531Sequence Status: Not CompleteSequence: View Nucleotide Sequence and design PCR primersNumber of Proteins: 1Organism Name: Human herpesvirus 5

Strain Details for Human herpesvirus 1 Strain 17

Genomes: Genome: Af513130 | Genome: Ay788102 | Genome: Ay818266 | Genome: Ay999217 | Genome: D00373 | Genome: Fj593289 | Genome: Gu057933 | Genome:He582223 | Genome: Jn555585 | Genome: M19119 | Genome: M19120 | Genome: M19121 | Genome: M19122 | Genome: M24357 | Genome: Nc 001806 |Genome: S41948 | Genome: S41949 | Genome: S41950 | Genome: S41952 | Genome: S41970 | Genome: X04467 | Genome: X04614 | Genome: X06461 |Genome: X14112 |

Strain Information

Genome: AF513130

Genome: AY788102

Genome: AY818266

Home GBrowse Search Results Strain Details (17)

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Page 1 of 1http://www.vipr-dev.org/cgi-bin/gb2/gbrowse/herpes/?ref=NC_001806;start=1;stop=152261










5 kbp

upload_23268


Pfam domains

IEDB epitopes

DNA/GC Content

Overview

Region

Details

File Help













5 kbp

upload_23268


Pfam domains

IEDB epitopes

DNA/GC Content

Overview

Region

Details

File Help




Herpesviridae Annotations: 152.3 kbp from NC_001806:1..152,261

Browser Select Tracks Snapshots Custom Tracks Preferences

Custom Tracks[Help with uploading custom tracks]

There are no tracks yet.

Add custom tracks : [From text] [From a URL] [From a file]

Create a new trackNC_001806 10000 20000 reactivation

Upload Remove


File Help

Herpesviridae












5 kbp

upload_23268


Pfam domains

IEDB epitopes

DNA/GC Content

Overview

Region

Details

File Help


view genomes in gbrowse · 2020-04-20 · annotations of herpesviridae and poxviridae viruses...

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