Motif Collection

Motif Collections are a specific subtype of the general Collection data type that can only contain Motif objects. Motif Collections are mainly used to limit the application of certain operations and analyses to subsets of motifs, but they can also be used to import motifs from a file or return results from a motif discovery method.

All Motif Collections will appear in the "Motifs" panel in MotifLab's GUI, provided that you have selected to display "Motif Collections" using the drop-down menu in this panel. You can create new Motif Collections by pressing the "+" button in this panel and then selecting "Motif Collection" from the appearing menu, or you can go to the "Data" menu in the top menu bar and select "Add New ⇒ Motif Collection".

Creating Motif Collections

As described in the general section on collections, Motif Collections can be created by explicitly listing the names of motifs to include, using condititions to select motifs based on property values or values in Numeric Maps, or importing motif collections from files. In addition, MotifLab comes bundled with several predefined collections of motifs that can be imported, and Motif Collections can also be based on sequence support in motif tracks.

Predefined Motif Collections

MotifLab comes bundled with several predefined collections of motifs from publicly available databases, including e.g. TRANSFAC Public and JASPAR. In the GUI you can create such collections by selecting "Add New ⇒ Motif Collection" from the "Data" menu and then go to the "Predefined" tab. This will display a list of available collections. To import motifs from a collection, simply select the collection in the list and press "OK" (or double-click on a collection in the list). When you select a predefined collection from the list, the resulting collection object will automatically be named after the chosen motif collection, as shown in the text box at the top of the dialog. If you want to specify your own name for the new collection, you can change it in the text box before pressing "OK".

Importing a predefined collection of motifs will both create the new collection object and also create motif objects for all motifs defined in the collection. If the collection contains motifs with the same name as already existing motifs, the existing motifs will be replaced without notice.

The general syntax for importing predefined motif collections in protocols is:

Examples

You can add your own custom motif collections to the "predefined" list by right-clicking on the collection in the motifs panel and selecting "Save As Predefined" from the context-menu. Enter a name for the collection to use in the list and press "OK".

Collections based on motif occurrences

Motif collections can be based on motifs that have a certain sequence support in a motif track. By sequence support for a motif we mean the number of sequences that contain at least one occurrence of that particular motif. For example, one could create a collection with motifs that occur in at least 20 sequences or in 80% of all sequences.
In the GUI you can create such collections by selecting "Add New ⇒ Motif Collection" from the "Data" menu and then go to the "From Track" tab. First select the motif track from the drop-drop down menu at the top, then select the comparator function (=,<,<=,>,>=,<>,in) and target value from the bottom menus. The target value can be an absolute number or a relative percentage number (in which case the value should be between 0 and 100), and the value can either be a literal number or a numeric data object (Numeric Variable or Motif Numeric Map).
The general syntax for creating such motif collections in protocols is the following:


Examples