To install Teolenn, go to the Teolenn installation page and follow the detail procedure.
Create a folder where to put all your files. Next in this folder download the genome reference file (fasta format) and the masked genome (fasta format).
Create your design file (xml format) either from scratch using the documentation pages or by using the template design file we provide. The better is to create the design file in the same folder than genome files.
In the design file first edit the general parameters. Choose the start position between 0 or 1. This is important because this will help you make the link with annotations files. Choose the length of the oligonucleotide you want to design. Then fill the relative location to the design file for your genome files.
Next edit the sequencefilters and measurements. Pay attention that both values of the "skip" parameter is set to "false". We advise to use both the redundancy and Sequencexn filters. For the measurement you can add oligosequence, tm, %gc, complexicity and unicity. If you don't know which parameter to provide for maxprefixlength you can let it set to 30.
For measurementfilters and selector you can set the "skip" parameter to "true". Then launch the teolenn program for example as follow.
$ sh ../teolenn/teolenn.sh -log design.log design.xml
This first run has created the whole probe collection and apply a first general filter to discard redudant oligonucleotides and non classical bases. You can now access the statistics of all the parameter calculated for the probe collection in the "filtered.stats" file. This file display each parameter in column with an histogram distribution of the values and max, min, mean, median and standard deviation calculated.
These value are helpful to set up threshold on probe collection to discard low quality probes. To do so open the design.xml file. First put the skip parameter of sequencefilters and measurements to "true". Next edit the measurementfilters section and first put the skip value to "false". For each measurement you can edit threshold based on the statistical distribution obtained.
Now, you can launch teolenn another time. The probe collection is already done so that only the probe filtration step will be performed. This step is now very quick. At the end you can access the number of probe remaining in the filtered.mes file to compared with the number of oligonucleotide in the collection found in the oligo.mes file.
Now that you have filtered your probe library according to your needs, the final step is to perform the probe selection. To do so edit the design.xml file and put all skip tag to true except for the last one (selector). Only the selection step will be done each time you will launch Teolenn so that you can test several selection parameter configurations.
For a tiling design add "tiling" to the "name" tag and set the two parameters specific for this design: windowLength and windowStep. The first give the size of the tiling window. The second give the step of the tiling path.
Next set up the weight of each of the parameter to be taken into account for the final score calculation. Then launch the program. The final design probe can be retrieved in the select.mes file.