Sequence Partition

Sequence Partitions are a specific subtype of the general Partition data type that can only contain Sequence objects.

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

Creating Sequence Partitions

As described in the general section on partitions, Sequence Partitions can be created by explicitly listing the names of sequences to include in each cluster, or by using assignment rules to select which sequences to include in each cluster based on their values in Numeric Maps. In addition, Sequence Partitions can also be based on the values of some sequence properties as described below.

Partitions based on sequence properties

Sequence Partitions can be created by clustering together sequences that have the same value for a selected sequence property.
Currently, only four such sequence properties are supported:

• organism: Cluster together sequences originating from the same organism.
• genome build: Cluster together sequences originating from the same genome build.
• chromosome: Cluster together sequences from the same chromosome.
• strand orientation: Divides the sequences into two clusters named "direct" and "reverse" based on each sequence's orientation.
  If the orientation of a sequence is not specified, it will be assigned to a third cluster named "undetermined".

In the GUI you can create such partitions by selecting "Add New ⇒ Sequence Partitions" from the "Data" menu and then go to the "From Property" tab and select the property from the drop-down menu. The general syntax for creating sequence partitions based on properties in protocols is the following:


Examples