NCBI Sequence Viewer

URL Parameters

URLs for Sequence Viewer can be configured to customize the display. Sequence Viewer can also be embedded as a component in another web page.

Here are examples of embedded instances of the Sequence Viewer.

And here is the full API manual for embedding.

For constructing URLs, use the baseURL is http://www.ncbi.nlm.nih.gov/nuccore/ <INSERT GI HERE> ?report=graph& <List-of-arguments>

Arguments and argument qualifiers:

1. mk=<position or range>|<marker name>|<color in RGB hex> Use the mk parameter to set a marker at a position or on a range of positions. Multiple markers can be set by separating the triples with a comma. Use an exclamation point ("!") after a triple to lock the marker. And the name and color parameters are optional. Examples:

   • mk=1000 puts an unlocked marker with default color and name at position 1000
   • mk=1000:2000 puts an unlocked marker with default color and name on the range 1000-2000
   • mk=1000:2000|TestMarker puts an unlocked marker with default color and the name "TestMarker" on the range 1000-2000
   • mk=1000:2000|TestMarker|00ff00 puts an unlocked marker with color 0x00ff00 and the name "TestMarker" on the range 1000-2000
   • mk=1000:2000|TestMarker|00ff00,3000:4000|TestMarker2|80ff10 puts an unlocked marker with color 0x00ff00 and the name "TestMarker" on the range 1000-2000 and another unlocked marker with color 0x80ff10 and the name "TestMarker2" on the range 3000-4000.
   • mk=1000:2000|TestMarker|00ff00,3000:4000|TestMarker2|80ff10! - same as above with a lock on "TestMarker2" .
   • Note: Special characters in marker names must be escaped properly usually with a \ prepended.

2. toolbar=<nspztcrh> A set of switches that let you include/exclude particular options the toolbar. They're all present by default and as soon as one is specified, then you must opt in for all the choices.

   • n - Name button
   • s - Search field
   • p - Panning buttons
   • z - Zoom slider & buttons
   • t - Tools menu
   • c - Configure menu
   • r - Reload button
   • h - Help button

3. embedded=panorama Shows only the top panel, the Overview panel, when used in the embedded model.

4. origin=<sequence position> - Set the sequence origin (Example: origin=5000)
5. v=<view ranges> - Set a specified visible range to a graphical panel (Example: v=1000:6000,100k:2m, 100K-2M, 100k..2M)
6. c=<colors list> - Set a specified color to a graphical panel (Example: c=0000FF,FFFF99)
7. rid=<BLAST RID> - Option to load BLAST results stored as an RID

8. theme=<theme list> - Set graphical display to a specific theme as a set of options in the order below(Example: theme=Default)

   • Parameter Order - {color, decor, content, layout, spacing, label, geneModel}
   • 0 - Compact - {0,0,1,0,1,0,2}
   • 1 - Default - {0,0,1,0,0,0,1}
   • 2 - Expanded - {0,0,1,0,2,0,0}
   • 3 - Details< - {0,0,1,0,0,1,0}
   • 4 - Fancy - {0,2,1,0,2,1,0}

9. content=<content list> - Set graphical display content (Example: content=0)

   • 0 - Defaults
   • 1 - Details
   • 2 - Assembly Details
   • 3 - Everything
   • 4 - Genes
   • 5 - Genes and SNPs
   • 6 - Genes and Proteins
   • 7 - Overview

10. color=<color list> - Set graphical display color style (Example: color=0)

    • 0 - Color
    • 1 - Greyscale
    • 2 - High Contrast

11. decor=<decor list> - Set graphical display decor (Example: decor=0)

    • 0 - Default
    • 1 - Arrows
    • 2 - CircleAnchor
    • 3 - Fancy
    • 4 - SquareAnchor

12. layout=<layout list> - Set graphical display layout (Example: layout=0)

    • 0 - Defaults
    • 1 - Level 1
    • 2 - Level 2
    • 3 - Level 3
    • 4 - Multi Level

13. spacing=<spacing list> - Set graphical display spacing (Example: spacing=0)

    • 0 - Normal
    • 1 - Compact
    • 2 - Oversize
    • 3 - Overview

14. label=<label position> - Set label position (Example: label=0)

    • 0 - Default (side)
    • 1 - Top
    • 2 - None

15. geneModel=<MergeStyle> - Set gene merge style (Example: geneModel=0)

    • 0 - No Merge
    • 1 - Merge Pairs
    • 2 - Merge All

16. alncolor=<on/off list> - Enables alignment coloration in the graphical display (Example: alncolor=on,off)

17. flip=true - Flips the strand (Example: flip=true or flip=false,true to flip strand in the second graphical panel)
18. select=<feature ids> - Brings up a Marker Dialog (Example: select=00142d2b-000000c8-00000a44-0103-a209ee38)
19. seq=from:to - Brings up a Sequence Text window (Example: seq=2000:7000)
20. search=<search term> - Brings up a Search Dialog (Example: search=GEN*)
21. vm=true - Brings up a Marker Dialog (Example: vm=true)
22. naa=<accession list> - Option to load external named annotations (Example: naa=NA000000003,NA000000004,NA000000004:renderer_name)
23. key=<NetCache key> - Option to load external data from the NetCache
24. URL=<URL to an external file> - Option to load external data from a publicly accessible site (see Load External Data )
25. DEPRECATED from=<sequence position>&to=<sequence position> - Set a specified visible range to a graphical panel. (Example: from=1000&to=8000)
26. DEPRECATED in version 2.7 m=<markers positions> - Set markers to specified positions (Example: m=1000,25000). An exclamation point ("!") after the marker position will make it locked.
27. DEPRECATED in version 2.7 mn=<markers names> - Set names for the markers (Example: mn=Marker 1,SNP #1)