Navigate through sequence

Navigation controls

Sequence Viewer has the following navigation controls:

Pan arrows

Pan arrows

You can move the display left or righ by using the left or right arrow icons on the toolbar, respectively.

Pan by dragging

You can also pan the view left and right simply by clicking and dragging on the image itself.

Zoom slider with zoom out and zoom in buttons

Zoom slider

You can zoom in/out on the visible range by dragging the slider left/right. Clicking on the - or + allows to jump to the higher/lower level of zooming.

Zoom to sequence button

Zoom to sequence

Zoom to sequence button allows you to jump (on the visible range) to the nucleotide sequence level.

Nucleotide sequence

Jump left and Jump right arrows for each track

Jump arrows

You can navigate between the visible objects of the track by clicking the navigation buttons (jump arrows). Clicking the buttons sets the marker to the closest object position relative to the center of the screen. The consecutive clicks move the marker along the visible object range and between the objects relative to the marker’s position.

You can hold ‘Ctrl’ button while clicking the navigation buttons to skip through the exons of the multi-exon gene or through the segments of the multi-segmented alignments.

Navigating gene tracks

Open chromosome 1

Move to the coordinate 97,373,550.

Zoom to the nucleotide sequnce level.

Do not forget to configure your Sequence Viewer to show gene tracks.

For simplicity all other tracks in the example are hidden.

gene navigation

Click on the right jump arrow. Marker will be set at the beginning of the next exon.

gene navigation 1

Click on the right jump arrow. Marker will be set at the end of the exon.

gene navigation 2

Click on the right jump arrow. Marker will be set at the beginning of the next pseudogene.

gene navigation 3

Navigating alignments

Open chromosome 1

Move to the coordinate 97,540K.

Zoom to the nucleotide sequnce level.

Do not forget to configure your Sequence Viewer to show alignments.

For simplicity all other tracks in the example are hidden.

alignment navigation

Click on the right jump arrow. Marker will be set at the beginning of the next alignment.

alignment navigation 1

Click on the right jump arrow. Marker will be set at the end of the same alignment.

alignment navigation 2

Click on the right jump arrow. Marker will be set at the beginning of the next alignment.

alignment navigation 3

Navigating SNPs

Open chromosome 1

Move to the coordinate 86,728,370.

Zoom to the nucleotide sequnce level.

Do not forget to configure your Sequence Viewer to show SNPs.

For simplicity all other tracks in the example are hidden.

snp navigation

Click on the right jump arrow. Marker will be set at the next snp.

snp navigation 1

Click on the right jump arrow. Marker will be set at the beginning of the next indel.

snp navigation 2

Click on the right jump arrow. Marker will be set at the next snp.

snp navigation 3

Click on the right jump arrow. Marker will be set at the end of the indel.

snp navigation 4

Click on the right jump arrow. Marker will be set at the next snp.

snp navigation 5

Context-dependent navigation

The behavior of jump arrows is context-dependent and changes when you change rendering options. Previously we showed gene track navigation using show all option.

Open the same example and choose Gene bar only rendering option in the Genes/products tab of the Configuration dialog.

configure 1

configure 2

gene navigation 4

Click on the jump arrows and watch the Sequence viewer navigating genes only and skipping all the features.

gene navigation 5

gene navigation 6

Range tooltip

Select a range and place the cursor on the coordinates ruler. Range tooltip will be displayed.

Range tooltip

Tooltip presents to you with the following navigation commands:

  • Zoom on range - allowing you to to zoom to the level when the selected range is expanded to the visible range
  • Zoom to sequence - zooming to the nucleotide sequence level on the selected range

Range context menu

Select a range, place the cursor anywhere in the selected range, and click on the right mouse button. Context menu will be displayed

Range context menu

Context menu presents to you the following navigation commands:

  • Zoom in - jump to a lower zoom level on the selected range
  • Zoom out - jump to a higher zoom level on the selected range
  • Zoom to sequence - zooming to the nucleotide sequence level on the selected range
  • Zoom on range - allowing you to to zoom to the level when the selected range is expanded to the visible range
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Last updated: 2015-06-05T11:56:56-04:00