The measurement section of design file

This section of the design file define the measurements to compute on generated oligonucleotides. The following source show the structure of a typical measurement section of the design file:

<measurements skip="false">
	<measurement>
		<name>oligosequence</name>
	</measurement>
	<measurement>
		<name>tm</name>
	</measurement>
	<measurement>
		<name>%gc</name>
	</measurement>
	<measurement>
		<name>complexity</name>
	</measurement>
	<measurement>
		<name>unicity</name>
		<parameters>
			<parameter>
				<name>maxprefixlength</name>
				<value>30</value>
			</parameter>
		</parameters>
	</measurement>
</measurements>

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 measurement.

Each measurement, add a column to the measurement file(oligo.mes). The standard version of Teolenn contains 7 measurements:

• chromosome: Add the chromosome of the oligonucleotides sequence to the measurement file.
• oligostart: Add the start position of the oligonucleotides on the chromosome.
• oligosequence: Add the sequences of the oligonucleotides.
• tm: Add the melting temperature of the oligonucleotides.
• %gc: Add the percent of gc of the oligonucleotides.
• complexity: Add a complexity value based on the genome masked.
• unicity: Add the unicity value for each oligonucleotides.

On this 10 measurements two (Chromosome and oligostart) are automatically added to measurement file.

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

The chromosome measurement

• Name: chromosome
• Description: Get the chromosome source of an oligonucleotide.
• Parameters: None.
• Use external tool: No.
• Automatically added to measurements file: Yes.

The oligstart measurement

• Name: oligostart
• Description: Get the start position on the chromosome of the probe.
• Parameters: None.
• Use external tool: No.
• Automatically added to measurements file: Yes.

The oligosequence measurement

• Name: oligosequence
• Description: Get the sequence of the probe.
• Parameters: None.
• Use external tool: No.
• Automatically added to measurements file: No.

The complexity measurement

• Name: complexity
• Description: Get a complexity value using masked genome created probes.
• Parameters: None.
• Use external tool: No.
• Automatically added to measurements file: No.

The %GC measurement

• Name: %gc
• Description: Get the percentage of GC bases in the oligonucleotide sequence.
• Parameters: None.
• Use external tool: No.
• Automatically added to measurements file: No.

The unicity measurement

• Name: unicity
• Description: Get the minimum length of the unique prefixes are located all along the genome in the oligonucleotide sequence.
• Parameters:
  • maxprefixlength: The maximum prefix length to search in all the genome.
• Use external tool: gt (genometools).
• Automatically added to measurements file: No.

Use external measurements

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

<measurement>
	<name>mymeasurement</name>
	<class>com.example.mymeasurement</class>
</measurement>