NCBI

Sequence Viewer v.2.0

Tips and documentation for the NCBI Sequence Viewer

Table of Contents

  1. Background
  2. Quick start
    1. Overview
    2. Navigation through sequence
    3. Default displays
    4. Representative displays
  3. Detailed description of visual components
    1. The common NCBI menu panel
    2. The Sequence Title Panel
    3. The Overview Panel
    4. A Sequence Text Panel
    5. A Sequence Graphical Panel
    6. The NCBI footer
  4. Configure Panel
  5. Access by URL
  6. Compatible browsers
  7. Sequence Viewer Development Team

Background

The NCBI Sequence Viewer (http://www.ncbi.nlm.nih.gov/projects/sviewer/) is being phased in to replace the graphical display option available from the Nucleotide and Protein databases. The functions included with the first release of this viewer are limited. As new functions are released, they will be documented here.

Quick start

This section summarizes the basic steps to control the sequence being viewed, and to navigate through that sequence. Explanations are based on the default options.

Overview

Click on this link for access to NCBI Sequence Viewer.

Start screen
Figure 1. Start screen

Enter an accession or gi in the Accession box and press enter. The default result (Figure 2) now includes two sequence-based panels:

  1. Overview Panel (top)
  2. Graphical Panel (below)

Default view with two panels
Figure 2. Default view with two panels

Please note that the overview panel contains a tabbed selection window that controls the extent of the display in the lower graphical panel .

The lower panel reports the coordinates of the sequence being displayed, and diagrams the placement of the features annotated within that range.

The region of the sequence displayed in any view panel below the Overview Panel is controlled by the tabbed grayed box (selection window) outlined in a color that matches the color used to outline the secondary view panel. To expand or contract the selection window, hover over the small boxes (with arrowheads) , toward the top of the selection window, and move the boxes when appears. To move to a new location, drag the box using the tab at the top of the selection window.

No matter what the type of view panel being displayed, you can alter the sequence display by entering the sequence coordinates in the Position box . A tool tip is attached to the word Position, indicating that ranges may be defined in two ways:

  1. begin-end or
  2. center position:length.
Values should be entered without commas, and k or m can be used to indicate kbp or Mb, respectively.

You can also move up or downstream by clicking on the arrow keys.

Graphical panel
Figure 3. Graphical panel

In a graphical panel (Figure 3), you can alter the display by moving your cursor to the top or bottom of the display (a hand will appear) and dragging the window to the left or right. The selection window in the overview panel will move coordinately. You can also move the selection window in the overview panel directly.

If you are in a graphical panel, you can open a different type of display, the Sequence text panel (Figure 4) by clicking on the icon.

Sequence text panel
Figure 4. Sequence text panel

In a sequence text panel (Figure 4), you can move the display upstream or downstream by using the left or right arrows on your keyboard, respectively. You may also move the selection window in the overview panel. The displays in the graphical and sequence panels are independently controlled.

You can zoom in and out in a view panel in several ways

  1. Zoom in
    1. Magnifying glass icon with the plus sign
    2. Keystrokes: "+" or lower case "z"
  2. Zoom out
    1. Magnifying glass icon with the minus sign
    2. Keystrokes: "−" or upper case "Z"
  3. Zoom to sequence
    1. "ATG" icon in the graphical panel
    2. Keystrokes: "*"

Default displays

Several features are displayed in the overview and graphical panels. These are distinguished both by position in the panel and by the color assigned to each. These colors can be altered by use of the Configure Panel . This example is based on a subsequence of AL020997.1

Colors.
Figure 5. Colors.

  1. Gray − the whole sequence.
  2. Green − position of part of the gene feature, with the locus_tag and orientation displayed
  3. Blue − position of some exons (thicker section) and introns (thinner section) of the RNA, when translated, that would result in CAI20567.1
  4. Red − position of part of a regions (thicker section) and introns (thinner section
  5. Black − any other feature type (variation, makers, regulatory sites)
  6. Blue − a selected RNA feature (click on the feature to select it) displaying mRNA coordinates of the sequence

Representative displays

  1. Protein sequence: gi|56158846 Note that the default view panel is sequence text.
  2. Viral genome: AC_000020, graphical and sequence views and 2 markers Note that one of the markers (4800) is in the region of overlap of the two view panels. Note also the color matching of the marker icons and the color matching of the control panels for each view panel and its tabbed selection window in the overview panel.
  3. Human chromosome: NC_000001 Note that in the display of a chromosome, a histogram of gene density is provided in the overview panel. The default for the view panel is graphic.
  4. Human contig, 4MB: NT_011515, first 30k in graphical view This is an example of setting a graphical view panel of 30kb via the URL
  5. Human RefSeq for beta globin: NG_000007 Note both the graphical display of the placement of regulatory regions (black), a gene (green), an mRNA (blue) and a coding sequence (red). Details about each feature icon are provided via mouseover.
  6. A segmented set: AH000039
  7. RefSeq mRNA: NM_198471.2
  8. MGC mRNA: BC066124.1
  9. Trace ti=555

Detailed description of visual components

Display resulting from the URL constructed as /projects/sviewer/?id=NG_005895.1&v=5827:1000;f:80,2642..6835;g;s:077d765e-00000e63-0000ad76-010a-a6104eb4&m=6095,3566.

Common view.
Figure 6. Common view.

Figure 6 shows six sections of a display:

  1. The common NCBI menu panel with a help button
  2. The Sequence Title Panel
  3. The Overview Panel
  4. A Sequence Text Panel
  5. A Sequence Graphical Panel
  6. The NCBI footer

NCBI Menu Panel.
Figure 7. NCBI Menu Panel.

This panel contains:

  1. Links to a subset of resources of NCBI,
  2. Name and version of Sequence Viewer
  3. Help button to display this help document.

The Sequence Title Panel

Sequence Title Panel.
Figure 8. Sequence Title Panel.

The Sequence Title Panel includes:

  1. The title of the sequence.
  2. The gi of the sequence, its source (GenBank, RefSeq, etc.) and the accession.version.
  3. Accession box. Enter the accession or gi of a sequence and press enter to display it.
  4. Refresh Button. Clicking on this will refresh all panels.
  5. Link Button. Create the URL that will generate the current view.

The Overview Panel

This panel includes several functions to control your display and position within the sequence.

The Overview Panel.
Figure 9. The Overview Panel.

The Overview Panel includes:

  1. New Graphical panel. Click on this button to open a new graphical view based on the position of the current view.
  2. New Sequence panel (ATGC). Click on this button to open a new sequence view starting from the position of the current view.
  3. Shift Origin box. Enter a value and press "Enter" to shift the origin of all rules.
  4. Theme menu. Select your preferred theme for visible elements.
  5. The wrench button. Click on this button to open the Configure Panel to customize your display.
  6. The inverted triangle/+ button. Click on this icon to create a new marker (at the left of the display) and a new window to control the marker's position. Up to 5 markers (distinguished by colors) can be created.
  7. Marker coordinate box. Displays the current position of the marker indicated by its color at the left of the window. You can enter a new value and press enter to move the marker.
  8. Delete marker button. Click to delete that marker.
  9. Tab to move the graphical/sequence view position. Click and drag to shift the position without changing the window size
  10. Handle to reset the left boundary of the graphical/sequence view. Click and drag to adjust the starting position.
  11. Location box. This box represents the width and position of a graphical/sequence view on the complete sequence. The boundary of the box is color-coded to match the boundary of the view panel it represents.
  12. Handle to reset the right boundary of the graphical/sequence view . Click and drag to adjust the end position.
  13. Marker icon. Click and drag to move the marker. The new position will be displayed in the color-matched marker coordinate box.
  14. Sequence overview image. This display is controlled by the Theme menu and the Panorama Control Panel.

A Sequence Text Panel

The Text Panel.
Figure 10. The Text Panel.

The Sequence Text Panel includes:

  1. New Graphical panel. Click on this button to open a new graphical view based on the position of the current view.
  2. The inverted triangle/+ button. Click on this icon to create a new marker (at the left of the display) and a new window to control the marker's position. Up to 5 markers (distinguished by colors) can be created.
  3. Position label. Click to switch between methods to enter position, either as a range (19.5k-20.5k) or center position and length (20K:1000).
  4. Position entry box. Enter a position and press enter to change the position of sequence to display.
  5. Refresh Button. Click to refresh this panel.
  6. Left arrow. Click to move left/upstream the number of nucleotides corresponding to 1/10 of your display window.
  7. Right arrow. Click to move right/downstream the number of nucleotides corresponding to 1/10 of your display window.
  8. Zoom in. Click to zoom in.
  9. Zoom out. Click to zoom out.
  10. @@@@. @@@.
  11. Collapse the sequence panel..
  12. Delete the panel.
  13. Coordinates. Range of the sequence being shown on that line.
  14. Coordinates. Numbering by 10 for the line shown.
  15. @@@. @@@
  16. @@@. @@@
  17. Position of marker. This box can be dragged to move the marker. This position of the marker will be updated in the Overview panel.
  18. Exon highlights. Different coloration to indicate exon position.
  19. Reflector. Bar (color-coded) to indicate how the range of sequence covered in a graphic panel corresponds to the range displayed in this sequence panel.

A Sequence Graphical Panel

The Graphic Panel.
Figure 11. The Graphic Panel.

The Panel includes:

  1. New Sequence panel (ATGC). Click on this button to open a new sequence view starting from the position of the current view.
  2. The inverted triangle/+ button. Click on this icon to create a new marker (at the left of the display) and a new window to control the marker's position. Up to 5 markers (distinguished by colors) can be created.
  3. Position label. Click to switch between methods to enter position, either as a range (19.5k-20.5k) or center position and length (20K:1000)
  4. Position entry box. Enter a position and press enter to change the position of sequence to display.
  5. Refresh Button. Click to refresh this panel.
  6. Left arrow. Click to move left/upstream the number of nucleotides corresponding to 1/10 of your display window.
  7. Right arrow. Click to move right/downstream the number of nucleotides corresponding to 1/10 of your display window.
  8. Sequence text icon. Click to display sequence (100 nucleotides) overlaid on the graphical view.
  9. Zoom in. Click to zoom in.
  10. Zoom out. Click to zoom out.
  11. Theme menu. Select your preferred theme for visible elements.
  12. The wrench button. Click on this button to open the Configure Panel to configure the panel.
  13. Collapse the panel.
  14. Delete the panel.
  15. Scrollable part of the graphical view. Click and drag to move up or downstream.
  16. Marker control. Click and drag to move the marker.
  17. Coordinate label. This display results from clicking on the mRNA feature.
  18. Feature label. This display results from mouse over on the mRNA feature.
  19. Reflector. Bar (color-coded) to indicate how the range of sequence covered in a sequence panel corresponds to the range displayed in this graphical panel. In this example, the sequence panel covers 1 kb between 19.5K and 20.5K

The NCBI Footer Panel.
Figure 12. The NCBI Footer Panel.

The footer includes:

  • The links to the Contact, Copyright, Disclaimer, Privacy and Accessibility information; NCBI address.
  • Data of last updating of NCBI Sequence Viewer and its revision number.

    • Configure Panel

    The Configure Your Display window.
    Figure 13. The Configure Your Display window.

    This box opens when you click on the icon shaped like a wrench in the overview or graphical panels. You can drag it to another position so it will not mask what you want to display,

    1. The title indicates which panel will be configured (Overview or Viewport)
    2. Delete button. Click to close this window and ignore any changes.
    3. Set of configuration elements:
      • Color
        1. default colors are gene for genes, blue for RNAs, red for coding regions, black for any other feature.
        2. Grey scale: differentiation is provided by grey scale.
        3. High contrast:
      • Decoration. Several options are provided to indicate directionality of features. Sequence viewer displays all annotations under the sequence, so orientation is not indicated by position over or under a sequence, but by arrows.
      • Content
        1. Default: Genes, mRNAs, CDS, markers
        2. Assembly details: component sequences assembled to create the displayed sequence
        3. Everything: all features annotated on the sequence
        4. Genes: Genes, mRNAs, CDS
        5. Genes, Markers; Genes, mRNAs, CDS, markers
        6. Genes, SNPS: Genes, mRNAs, CDS, SNPs
      • Layout
        1. Default: annotation on the displayed sequence only
        2. Level 1: same as default
        3. Level 2: annotation on components of the displayed sequence
        4. Level 3: annotation on components of components of the displayed sequence
        5. Multilevel: annotation from all levels
      • Spacing
        1. Default
        2. Oversize: bars are twice as thick as the default
        3. Overview: bars are half the thickness of the default
    4. Close button. Click to close this window and ignore any changes.
    5. Apply button. Apply changes you made. The window remains open.

    Access by URL

    The base URL is http://www.ncbi.nlm.nih.gov/projects/sviewer/?<List-of-arguments>

    Arguments and argument qualifiers:
    1. id - Required to identify the sequence
      • Processes nucleotide gis, protein gis, accessions, accession.versions ?id=NG_005895
    2. v - Optional; opens a new viewport for a bounded range (start-stop) or opens a new viewport of a given size centered at a position (centerpoint:length)
      • Range as a start-stop ?id=NG_005895&v=1K-3K
      • Centered position as centerpoint:length; default additional view (viewport) is graphical if ;f is added, the viewport will be text ?id=NG_005895&v=4.5k:1k
      • Content qualifier, options 0,1,2,3,4,5, corresponding to the content choices in the Configure Panel , where 0=default; 1=Assembly details; 2=Everything; 3=Genes; 4=Genes,Markers; and 5=Genes, SNPs. Thus, to open a graphical panel showing gene and variation (SNP) features: ?id=NG_005895&v=5.5K-7K;g;content:5
      • Layout qualifier, options 0,1,2,3,4, corresponding to the layout choices in the Configure Panel , where 0=default; 1=Level 1; 2=Level 2; 3=Level 3; 4=Multilevel;
      • Spacing qualifier, options 0,1,2,3, corresponding to the spacing choices in the Configure Panel , where 0=default; 1=Oversize; 2=Overview Thus, to open a graphical panel showing gene and variation (SNP) features, with overview spacing ?id=NG_005895&v=5.5K-7K;g;content:5;spacing:2
    3. m - Optional: sets a marker at a defined position, in one or more viewports

    Options for reporting positions include full integers (without commas), or float with k for 1000, m for 100000. Use of k or m is NOT case-sensitive.

    Compatible browsers

    1. MS Windows
      1. Microsoft Internet Explorer 7
      2. Firefox 2
      3. Opera 9.5
    2. Mac OS X
      1. Firefox 2
      2. Safari 3
    3. Linux
      1. Firefox 2

    Sequence Viewer Development Team

    The Sequence Viewer was created entirely at NCBI using the NCBI C++ Toolkit and JavaScript components. The code base for the Sequence Viewer is shared with Genome Workbench, and the development team will be working on providing complete integration of Genome Workbench components for the web.

    The Sequence Viewer development team includes: