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How to use DASher

  • Go to the webstart page and launch DASher.

    It will take a few seconds for Java to load, and you will be asked to trust the certificate (please do—it's from me!). If your browser asks you what to do with the .jnlp file, tell it to use the javaws program. You'll need to know where your copy of the javaws program is, of course.

    If Java launches, but complains about the version, then you may not be running Java version 6 (1.6), which is required for DASher. You can download it here.

    If Java doesn't launch at all, then it's possible you don't have Java installed. You can get it here.

  • Enter a protein ID in the search box on the toolbar.

    This will be in the upper-left corner of the window. Hit return or press the Send ID button.

    Tracks of annotations from DAS servers will start to appear. You may need to resize the window slightly to get the vertical scrollbar to appear (due to an unresolved display bug). Scroll down to see the rest of the tracks.

In the main window

When the mouse is in the main part of the window, over the tracks:

left-clickzoom in and center at that point
right-clickzoom out
middle-clickshow the popup window for a track. On a Mac, you can ctrl-click instead.
click and dragzoom in on a region

In the status window

DAS sources status window

The first thing you will see after typing in a Uniprot ID and hitting 'Send ID' will be the status window.

To each Uniprot-compatible, feature-containing DAS source that was listed at the DAS Registry, DASher will send a request asking for annotations connected to the given ID. The status window shows the current state of that request, from "Requesting" to "Retrieving" to "Response received".

And if there was some problem with the request, you will see information about that. For example, if DASher hasn't heard back from the source in 15 seconds, you will see "Request timed out". Or, as shown in the picture above, you might see "Malformed DAS XML", which usually means that the DAS server is offline.

The other type of information shown in the status window is the number of features returned by the source. More specifically, it is the number of positional features returned by the source. A positional feature is one which corresponds to a particular part of the sequence and has a start and stop position as part of the annotation. Non-positional features such as journal references are not currently displayed in DASher, and so that's why you may see some sources shown with "Response received" but with a feature count of 0 and no track present in the main window.

In the options window

DASher options window

Customizing how tracks are displayed

On the left is a list of all of the DAS sources with feature annotations for the current protein. Each has a checkbox which toggles the visibility of that track. You can re-order the tracks by clicking on a track name and pressing the Move Up and Move Down buttons.

On the right are controls for the appearance of the two types of tracks: segments, which are the typical, box-style features, and curves, which are the line graphs. In the upper right, you can toggle the visbility of all of the segments or all of the curves, and you can set their track height (in pixels) by typing in a new value and hitting return.

There is also a checkbox for controlling the color palette DASher draws from when looking for which color to use for a particular feature type. By default, DASher will use the source's stylesheet color preferences, if available. If the box is unchecked, DASher will use its own, internal palette.

The advantage of using the stylesheet is that there is consistency in the display of a source's annotation across different DAS clients, but the disadvantage is that there is no consistency in the color used for a given feature type across tracks in the same DAS client. Unchecking the checkbox and using DASher's color choices overcomes this disadvantage because DASher will apply the same color to a given feature type regardless of which track that feature is part of.

Saving track configurations

Sometimes you've hidden certain tracks and rearranged their order, and you want to be able to come back to that view without having to do a bunch of clicking all over again.

Now it's possible to save and restore the order and visibility of tracks in a custom track configuration. Once you've arranged tracks to your liking, click the "Save" button and choose a filename to save the configuration to. Once that file is saved, you can later retrieve your custom configuration by clicking the "Restore" button and choosing the previously saved file.

If you'd like to make your own track configuration file outside of DASher, feel free. It's simply a tab-delimited text file with two columns: the track nickname and its visibility state. The order of the lines in the file corresponds to the order in which they will be displayed.

Note the currently custom track colors and track heights are not saved as part of a track configuration file, but this is capability is planned for a future release. If this is particularly important to you, send me an email and let me know!

In the track popup window

track information popup window

Middle-clicking on a track in the main window reveals a popup with more information about that track. At the top, there is a brief description of that DAS source. If you need more information, click on the button just below the description to launch your web browser and see the full details on the DAS source at the DAS registry.

The lower half of the popup shows a list of all of the features provided by this DAS source for the given protein. The name of the feature type is shown, along with its start and end coordinates and its color.

Colors for several common features have been pre-selected either by the track's stylesheet or by DASher; all other features are assigned a color randomly. You can override the color choice for a given feature type by clicking on the color swatch and then choosing a new one from the color picker. The new color will then be used for all features of that type in all tracks. If you want to go back to using default colors, click on the "Stylesheet colors" checkbox in the options window.

On the toolbar

DASher's main window toolbar
Protein IDenter the UniProt ID for the protein you want to see annotations for
Send IDdo the query you entered (or just hit return)
&ndashzoom out
=zoom to show the entire sequence
+zoom in
Center onenter a residue coordinate to center the display on
Current positionthe residue coordinate the mouse is currently over
Optionsshow the options window
Statusshow or hide the status window
Helplaunch a web browser and display this help page
Exportcopies the current display to the clipboard for pasting into a drawing program
Printprints the current display
Quitquit out of DASher

Other important information

Mismatch between the sequence version and the annotation version

Some tracks may appear with their name colored red (as opposed to the usual black). This indicates that the version of the UniProt sequence used for the annotation may not match the version of the UniProt sequence retrieved from UniProt. If this were the case, it's possible that the coordinates of some of the annotation would be incorrect.

It's important to note, however, that many DAS protein feature annotation servers do not properly implement the version tag. With those servers, you would still get a warning, but there may not actually be any annotation discrepancy. This is an issue of standards compliance which the DAS community is actively working to resolve.

Need more help?

Just email me!

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