The sequence filters section of design file

This section of the design file define the filter that Teolenn must apply on the sequences generated from the genome file.

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

<sequencefilters skip="false">
	<sequencefilter>
		<name>redundancy</name>
	</sequencefilter>
	<sequencefilter>
		<name>Sequencexn</name>
	</sequencefilter>
	<sequencefilter>
		<name>dummysequencefilter</name>
		<parameters>
			<parameter>
				<parameter>param1<parameter>
				<parameter>value1<parameter>
			</parameter>
			<parameter>
				<parameter>param2<parameter>
				<parameter>value2<parameter>
			</parameter>
		</parameters>		
	</sequencefilter>
</sequencefilters>

Each sequence filter is defined by:

  • A name.
  • A class if the sequence filter is provided by an external plug-in.
  • Some parameters that allow configure each filter.

The standard version of Teolenn contains 2 filters:

  • Sequencexn: filter all the sequence that contains other Nucleic Acid Code that A, T, G or C (case insensitive).
  • redundancy: filter all the redundancy oligonucleotides.

Note that this step can be skipped by setting the skip attribute to true in sequencefilters tag.

The Sequencexn filter

  • Description: This sequence filter filters all the sequence that contains other Nucleic Acid Code that A,T,G or C (case insensitive).
  • Parameters: None.
  • Use external tool: No.

The redundancy filter

  • Description: This sequence filter filters all the redundancy oligonucleotides.
  • Parameters: None.
  • Use external tool: SOAP.

Use external sequence filters

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

<sequencefilter>
	<name>sequencefilter</name>
	<class>com.example.mysequencefilter</class>
</sequencefilter>