The Genomatix Java Graphics Component

[Introduction] [Selection tree ] [Toolbar] [Main panel] [Navigation panel]

Introduction

All interactive graphic pages within Genomatix browser based software are implemented as Java applets, running within your web browser requiring a Java plug-in (also see our technical FAQs).

By default, the width of the applet is optimized for your screen width, so you might have to resize (i.e. maximize) your browser window to see the whole graphics.

All graphics within Genomatix software generally consist of four parts which are described below:

a selection tree to select elements to display or hide (left)
a toolbar with action buttons (top right)
a main panel with the main results and/or sequences (middle right)
a navigation panel with zoom- and scroll options (lower right)

The selection tree

To the left of the graphics there is a tree containing all elements that can be toggled on or off for display in the main panel. Tree hierarchies can be shown or hidden by clicking the + or - symbols respectively. Checkboxes provide the possibility to toggle the visibility of the elements. Depending on the type of program elements can be

all genes/loci/transcripts which were found on the sequence
all types of sequences elements annotated within ElDorado (like transcripts, promoters sets, SNPs etc)
transcription factor binding sites

The selection tree panel can be hidden completely by clicking on the top arrow between the selection panel and the right side of the graphics. It can be brought back to front by clicking on the lower of the two arrows.

The toolbar

The toolbar contains buttons

to perform general actions (like exporting complete results or parts of the graphics) and
special actions depending on the program (like aligning sequences, filtering transcription factor binding sites for higher matrix similarity)

The special action buttons are described on the help page of the corresponding program.

The toolbar usually shows buttons for the following general actions:

	exporting the complete result page to HTML (including all graphics in JPG format)
	exporting the graphics or a selected region to a certain format (JPG, PNG, TIFF, PNM), based on the current settings of zoom and element selection
	selection of a region which can then be exported
	recalculation of the layout, i.e. the graphics is displayed as it was set up by default

The main panel

The main panel contains the main analysis result, depending on the program output:

For the detailed graphics for a ElDorado request, it contains one sequence with all annotated elements (transcripts, promoters, SNPs, probes etc.) for this sequence fragment.
For the "Transcripts & Probe Sets" as well as "Comparative Genomics" tasks in ElDorado, the main panel shows all transcripts below each other, one transcript per line.
For MatInspector the main panel contains the sequence fragment including all found transcription factor binding sites.
For FrameWorker and the task "Search for common transcription factor binding sites", the main panel contains all input sequences with the common TF sites or modules.

In all graphics, the black and gray patterned line represents the sequence. Each scale line corresponds to 50 basepairs.

The navigation panel

navigation

The view on the sequence can be changed by using the zoom- and scroll element in the lower right part of the graphics. The navigation panel contains a scaled down version of the sequence and a red box which marks the currently selected part of the sequence that is visible in the main sequence panel above. By default, the whole sequence is displayed.

slider To zoom in or out, click on the red box in the navigation panel and adjust the box by reducing the size via its handles (the small white boxes top left and bottom right of the red box). The sequence in the main panel will adjust to the selected window.

If you want to scroll along the sequence, move the red box within the navigation panel by sliding it with the mouse to the desired position. Alternatively you can click anywhere inside the scrollbar to jump to the desired destination. Depending on your browser, the red box can also be moved via the arrows on the keyboard.