The selector section of design file

This section of the design file allow to specify the type of selection and to set the weight and other parameters for each measurement used for the design.

The following source show the structure of a typical selector section of the design file:

<selector>
	<name>tilling</name>
	<parameters>
			<parameter>
				<name>windowlength</name>
				<value>140</value>
			</parameter>
			<parameter>
				<name>windowstep</name>
				<value>140</value>
			</parameter>
		</parameters>
		
	<measurement>
		<name>%gc</name>
		<weight>0.150</weight>
		<parameters>
			<parameter>
				<name>reference</name>
				<value>0.33</value>
			</parameter>
			<parameter>
				<name>deviation</name>
				<value>0.14</value>
			</parameter>
		</parameters>
	</measurement>
	<measurement>
		<name>complexity</name>
		<weight>0.075</weight>
	</measurement>
	<measurement>
		<name>unicity</name>
		<weight>0.225</weight>
		<parameters>
			<parameter>
				<name>max</name>
 				<value>38</value>
			</parameter>
		</parameters>
	</measurement>
	...
</selector>

As Teolenn can use several algorithms for selection, you must specify the type of selector and its parameters.

Each measurement of the selector section is defined by:

  • A name.
  • A weight that define the weight of the measurement in the global score
  • Some parameters that allow configure the computation of the score for each measurement.

If a measurement is not present in the selector section, all the scores of this measurement will be at 0 as by default the weight of a measurement is equal to 0. In addition, extra parameters are sometimes needed to compute the score for a measurement. The next subsections summaries this parameters for score computation.

The selector type

Teolenn is modular and for the selection phase as for the previous phases, you have the choice of the selector to use. Currently, only the tilling selector is available but a selector for ORF microarray design is under development.

As for measurements and filters, the selector can be configured with parameters.

Tilling selector

  • name: tiling
  • Parameters:
    • windowlength: The length of the tiling windows
    • windowstep: Increment between two tiling windows. Must be > 1

The measurements parameters

This section contains the specifics parameters of measurements for the selection phase.

The tm measurement

  • name: tm
  • Parameters:
    • reference: The Tm value to be obtained. Can easily be set up to the Tm mean distribution.
    • deviation: The deviation around the Tm reference to be allowed. The best score will be given for Tm near the reference + ou - the deviation.

The %GC measurement

  • name: %gc
  • Parameters:
    • reference: The GC percent value to be obtained. Can easily be set up to the GC content mean distribution.
    • deviation: The deviation around the GC percent reference to be allowed. The best score will be given for GC percent near the reference + ou - the deviation.

The complexity measurement

  • name: complexity
  • Parameters: None.

The unicity measurement

  • name: unicity
  • Parameter:
    • max: Maximum of uniqueness value

The position measurement

  • name: unicity
  • Parameter: None.

Use external selector

Teolenn is a very customizable tool, you can use your own selector (see the developing plug-ins section for more informations). To enable your custom selector, you must add the full name of the main class (witch implements SequenceSelector) of your plug-in in the design file as shown in the following sample:

<selector>
	<name>myselector</name>
	<class>com.example.mymeasurement</class>
	...
</selector>