Tips & Tricks

  • If you have started a lengthy operation that you would like to cancel, you can normally do so by pressing the UNDO button in the toolbar.

  • If you have a very small computer screen (or very large screen), you can change the size of the sequence windows in the Sequence Browser by going to the "Configure" menu and select "Options...". In the Options dialog, go to the "Visualization" tab. Here you can specify the width you want for the sequence windows (in pixels). Also, if you feel that showing all three data panels (Features, Motifs and Data objects) at once makes the panels too small, you can go to the "View" menu and select "Data Panels → Show Tabbed" to show just one at the time.

  • If you use an operation to create or change a "non-visual" data object (not feature data tracks), a dialog will normally pop up to show you the results. However, if you hold down the SHIFT key while clicking the OK-button in the operation dialog, the results will not be presented in a popup dialog.

  • You can execute a single command in a protocol by placing the cursor on the line in the protocol editor and press CONTROL+Enter. If you hold down the SHIFT key simultaneously, you will suppress any dialogs that might popup to show you the results.

  • It is fully possible to create random collections in MotifLab, but since we have not added this functionality to any GUI-dialogs yet, you have to do it in a protocol script using one of the following commands:

    NewCollection = new Sequence Collection(Random:20)
    NewCollection = new Sequence Collection(Random:20%)
    NewCollection = new Sequence Collection(Random:20 from OtherCollection)
    NewCollection = new Sequence Collection(Random:20% from OtherCollection)

    The first of these commands will create a new collection of (at most) 20 sequences randomly selected from all the current sequences. The second command will select 20% of the current sequences for the new collection. The third and fourth commands will only consider sequences that are members of the Sequence Collection "OtherCollection" and select a random subset from this consisting of 20 sequences and 20% of the size of the OtherCollection respectively. These commands will work with any kind of collection (not just Sequence Collections), and it is possible to specify the collection size using a Numeric Variable rather than a literal integer. E.g. the commands:

    x = new Numeric Variable(10)
    NewCollection = new Motif Collection(Random:x%)

    will create a new random motif collection consisting of 10% of all currently known motifs.

    Update: In more recent versions of MotifLab it is also possible to use the "extract" operation on a collection to extract a random subset of it.

  • You can create entirely artificial sequences (not anchored to a specific genome) using the protocol command:

    NewSequenceName = new Sequence(1000)

    The argument in the parenthesis specifies the size of the sequence, and this can be given as an integer or with a Numeric Variable. Note that once you have annotated your sequences with any feature data, it is no longer possible to add new sequence objects.

  • Clicking on the memory-gauge (located to the left of the log-panel in the GUI) will run the garbage collector and free up memory.

  • Under the "configure server settings" option in the "configure datatracks" dialog it is possible to specify alternative mirrors for different servers that will be used if the original server is unavailable. However, it is also possible to specify that the mirror(s) should always be tried first, even if the original server is available. This option is especially useful if you have your own local mirror of the UCSC Genome Browser (which is the default server for most preconfigured tracks). To specify a primary server, simply type in the address for your mirror in the "Mirror sites" column and then follow this with the address of the original server (use commas to separate the entries). For example, if you would like to use the european mirror of UCSC Genome Browser located at "", type in "," in the "Mirror sites" field behind the "" entry.