Sequence Collection

Sequence Collections are a specific subtype of the general Collection data type that can only contain Sequence objects. Sequence Collections are mainly used to limit the application of operations and analyses to subsets of sequences, but they can also be used to import sequence definitions from a file.

All Sequence Collections will appear in the "Data Objects" panel in MotifLab's GUI. You can create new Sequence Collections by pressing the "+" button in this panel and then selecting "Sequence Collection" from the appearing menu, or you can go to the "Data" menu in the top menu bar and select "Add New ⇒ Sequence Collection".

AllSequences   (The default sequence collection)

MotifLab has a special sequence collection called "AllSequences" which is regarded as the default sequence collection. This collection is always present and it cannot be created or deleted (however, it will be hidden from the "Data Objects" panel in the GUI when it is empty). Neither can its contents be manipulated directly. The "AllSequences" collection will always contain all the currently defined sequences. Newly created sequences will automatically be added to "AllSequences" and deleted sequences will be removed from "AllSequences". Many operations and analyses require you to specify a sequence collection to apply the operation to, but if none are provided, the "AllSequences" collection will normally be assumed and the operation/analysis will thus be applied to all sequences.

Note that similar default collections do not exist for motifs and modules (i.e. there are no "AllMotifs" and "AllModules" collections). Hence, if you want to perform motif scanning with all currently defined motifs you must explicitly create a new Motif Collection containing all motifs and then refer to that collection in the motif scanning tool.

Although collections are normally regarded as unordered sets they are actually implemented as ordered lists even though the order is almost never an issue. Actually, the "AllSequences" collection is the only collection where the order is used for something in MotifLab, and it is also the only collection whose order can be manipulated. When outputting sequences they are normally output in the order they have in AllSequences, and this is also the order used to visualize the sequences in the GUI. You can reorder sequences in the GUI (and hence in AllSequences) by pointing at a sequence to give it focus and then use the CONTROL key plus ARROW UP or DOWN to move it, or right-click on a sequence and select "Reorder Sequences" from the context menu. Sorting sequences (either with the sort tool or the sort display setting) will also reorder sequences in the AllSequences collection.

Creating Sequence Collections

As described in the general section on collections, Sequence Collections can be created by explicitly listing the names of sequences to include, using condititions to select sequences based on property values or values in Numeric Maps, or importing sequence collections from files. In addition, Sequence Collections can also be based on sequence statistics as described below.

Collections based on sequence statistics

The statistic operation can be applied to feature tracks to calculate various statistics, such as counting the number of regions in each sequence, finding the largest value for each sequence in a numeric track or counting the number of A's for each sequence in a DNA track. This operation returns a Sequence Numeric Map with values for each individual sequence. As described in the general section on collections, collections can be created based on their values in Numeric Maps, so you can use the statistic operation to create a map and then create a collection from this map. However, it is also possible to perform this in one step and create a Sequence Collection directly from sequence statistics. (Actually, MotifLab will run the statistic operation in the background to create a map, and then use this to create the collection, but this is done automatically and the map is discarded afterwards).

In the GUI you can create such collections by selecting "Add New ⇒ Sequence Collection" from the "Data" menu and then go to the "From Statistic" tab. Press the "Select" button to define the statistic function (this will actually bring up the same dialog that is displayed for the statistic operation) and use the other menus to select the comparator function and target value(s).
The general syntax for creating sequence collections based on statistics in protocols is the following:


Examples