A Sequence Numeric Map is a data object that associates sequences with numeric values. It is a subtype of Numeric Map which again is a subtype of Map.

Creating Sequence Numeric Maps

Sequence Numeric Maps can be created by explicitly assigning values to named sequences, sequence collections, sequence partition clusters or sequence ranges. (See documentation under Maps and Numeric Maps). In addition, Sequence Numeric Maps can be created based on numeric properties of sequences or on statistics from feature datasets as described below.

Creating Sequence Numeric Maps based on sequence properties

In the GUI you can create such maps by selecting "Add New ⇒ Sequence Numeric Map" from the "Data" menu and then go to the "From Property" tab and select the property from the drop-down menu. All numeric properties can be selected, both standard and user-defined.

The general syntax for creating Sequence Numeric Maps based on properties in protocols is the following:

SequenceNumericPropertyMap = new Sequence Numeric Map(Property: <propertyName> )

Examples

# Create a numeric map based on the size of each sequence SequenceNumericMap1 = new Sequence Numeric Map(Property:length) # Create a numeric map based on the user-defined sequence property "geneExpression" SequenceNumericMap2 = new Sequence Numeric Map(Property:geneExpression)

Creating Sequence Numeric Maps based on feature track statistics

In the GUI you can create such maps by selecting "Add New ⇒ Sequence Numeric Map" from the "Data" menu and then go to the "From Statistic" tab. Press the "Select" button to bring up a second popup dialog where you can define the statistic function by selecting the feature track, type of statistic function and any conditions that may limit the function. Press "OK" and "OK" again to create the map.

The general syntax for creating Sequence Numeric Maps based on feature track statistics in protocols is the following:

SequenceNumericPropertyMap = new Sequence Numeric Map(Statistic: <statistic function> )

Examples

# Create a numeric map based on the GC-content of each sequence SequenceNumericMap1 = new Sequence Numeric Map(Statistic:"GC-content" in DNA) # Create a numeric map based on the number of TFBS regions in each sequence SequenceNumericMap2 = new Sequence Numeric Map(Statistic:"region count" in TFBS) # Create a numeric map based on average conservation score of each sequence SequenceNumericMap3 = new Sequence Numeric Map(Statistic:"average value" in Conservation)