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If you follow the "Detailed Graphics" link in the ElDorado overview, a new browser window will pop up showing a graphical representation of the search result, i.e. the sequence with all annotated elements together with zoom and navigation options.
For a detailed description of the annotated elements please see this page.
This interactive graphic page is implemented as a Java applet, running within your web browser requiring a Java plug-in (also see our technical FAQs).
The Java graphic consists of four parts:
For a detailed description of the general features of Genomatix graphics please check the graphics overview.
The black and gray patterned line represents the sequence. Each scale line corresponds to 50 basepairs.
Additionally, the line is flanked by red numbers indicating the currently visible portion of the sequence, i.e. the index of the first and last base pair respectively. Note that indices are relative to the contig to which it was mapped.
Each element annotated within ElDorado is displayed above, below or level with the patterned line depending on whether it was found on the positive or negative strand, or cannot be assigned to a specific strand. E.g. a yellow box above the line represents a promoter found in sense strand orientation.
Clicking on any annotated element on the sequence will bring up a tool tip with more information, especially start/end positions for this particular element. For example, clicking on the yellow box of a promoter will show information like promoter id, extent and a hyperlink to the Annotation & Analysis page in ElDorado from where this element can be analyzed further (e.g. by checking this promoter for transcription factor binding sites).
The density plot (which only appears if user data is present) displays the number of user elements covering a specific nucleotide position for each of the selected user data sets. The height of the peaks is normalized to the maximum value observed in the genomic region currently displayed in ElDorado.
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.
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.
To the left of the main sequence panel there is a tree containing all elements that can be toggled on or off for sequence display. Tree hierarchies can be shown or hidden by clicking the + or - symbols respectively. Checkboxes provide the possibility to toggle the visibility of
Each gene/locus on the sequence is listed and can be toggled off altogether. Additionally, if a gene/locus consists of several alternative transcripts, these can be toggled on/off separately by (de-)selecting the accession numbers from the list. Note: In this context a gene (or alternative transcript) is a unit consisting of the primary transcript, exons and UTRs. Thus, when a gene is deselected (selected), the symbols for the corresponding transcript together with its exons and UTRs will disappear (appear).
The top checkbox "Genes" can be used to toggle the view of all genes at once.
Note that the visibility of elements can also be handled using the legend symbols (as described below). Transcripts, exons and UTRs are visible only if either the gene to which they belong is selected or the elements of the specific type are switched back on.
The selection of annotated elements is at the same time a legend explaining which color represents each type element, and also displays the total number of elements found (in our example above there are 9 promoters found in the sequence). Checking an element type will switch the corresponding elements on the sequence on or off. E.g. deselecting the yellow promoters will switch off all promoters in the main sequence panel.
Currently the following types of elements are annotated in ElDorado and displayed in the graphics (see source of elements)
The toolbar contains a number of buttons for the following actions:
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exporting the complete result page to HTML (including all graphics in JPG format) |
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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 |
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selection of a region which can then be exported |
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recalculation of the layout, i.e. the graphics is displayed as it was set up by default |
These buttons allow to start a new ElDorado analysis with
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