VisSR

Sequence visualisation within the UEA sRNA Workbench is performed in the VisSR tool (pronounced visor). The tool may be run on its own or from other tools, e.g. miRCat. To open the tool choose ‘VisSR’ from the ‘Tools’ menu in the main Workbench window. Data is loaded into VisSR from the File menu.

VisSR showing a gene annotation for Arabidopsis thaliana

From top to bottom, the VisSR screen is divided into four sections:

Navigation controls

The sequence identifiers, e.g. chromosome ids, are shown in the drop-down list. Changing the value will load the sequence and recalibrate the display.Next to the list is an editable text-field within which base coordinates can be typed. When the two numbers are separated by a ‘-‘ the display is moved to the specified coordinates. If the numbers are separated by a ‘+’ then the second number specifies the width. Additionally, a ‘kb’ or an ‘mb’ may be included at the end of each number as short-hand for a thousand bases and a million bases respectively. For example, typing ‘1.5mb-2.5mb’ would move the display so that base number 1,500,000 lies on the left-hand side, and base number 2,500,000 on the right. The same result would be achieved by typing ‘1500kb+1mb’.Alternatively a text-based identifier can be typed and a search will be performed. This is useful for finding a specified gene when displaying annotations. For example, typing ‘AT1G01010’ when displaying chromosome 1 of Arabidopsis┬áthalianaproduces the view shown above.The ‘<<‘, ‘<‘, ‘>’, ‘>>’ buttons move the displayed range according to the currently displayed width. The ‘<<‘ button moves the display to the left by one whole screenful, while the ‘<‘ button moves the display by half a screenful. The other buttons move the displayed range to the right.

Sequence overview

The sequence overview is a number line which represents the current sequence, e.g. chromosome. The red box indicates the portion of the sequence which is displayed in the main data view below. The red box can be dragged using the mouse along the number line to move the displayed region.

Zoom control

The current zoom level corresponds to the location of the vertical notch on the horizontal line. To zoom out or in click on the notch and drag it to the left or right. As the zoom level is increased the main data view will change accordingly. Zooming is performed relative a fixed zoom point. To set the zoom point, click anywhere in the main data view. The position is indicated by a vertical grey line. The zoom point will remain in view when zooming. Clicking on the horizontal line away from the notch will cause the zoom level to jump.

Main data view

The display is divided into tiers, with a label on the left and the data on the right. The sequence is displayed in the first tier. To see the bases zoom all the way in. The second tier shows the view’s position on the governing sequence. Tiers can be added to the view using the items on the File menu. Loaded data is displayed using coloured graphic items (glyphs). The glyph for a strand aligned sequence displays an arrow at one end to indicate direction. If a label has been assigned to the glyph it will be shown when the zoom level is sufficiently high. Double-clicking on a glyph will cause the display to zoom in on it. A help-tip is displayed when the mouse hovers over a glyph. A context menu is displayed when either a tier’s label or a glyph is right-clicked.

A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices