The Disperse pipeline allows various settings to be made that affect the result of a design job. Also, the PieceMaker and ProbeMaker programs that carry out parts of the work, can be modified in several ways to fine tune the design. This is all done in the design settings file.
File name entries may be relative or absolute. Relative entries are interpreted relative to the location of the settings file itself.
A design settings file is made up of several property key-value pairs, one per line, such as:
key1=value1 key2=value2
The available properties and their meaning are described below for different categories of properties.
In the example settings file, the properties are organized so that the ones you are most likely to want to change are near the beginning of the file.
To create your own settings file, we recommend that you create a copy of the example file and adjust the properties according to your specifications.
This section lists the PieceMaker settings. For further details on the effect of these settings, refer to the original PieceMaker publication.
Specifies the filter to use at the digestion stage. Using a filter here will make the next two tasks go somewhat faster, as there will be fewer fragments to evaluate.
If omitted, no filtering will be performed at this stage.
The recommended filter to use here is:
net.genefront.selectortools.piecemaker.ops.impl.DuringCutFragmentFilter
Since this filter is applied before flap finding, it uses maxLength + maxFlap as a maximum length of fragments. Also, the snp distance is only applied at the 3' end, as the flap position is not yet set.
A flapfinder is responsible for finding suitable sites for cleaving off 5' ends of restriction fragments. The following settings are used to specify the flapfinder to use, and to set any parameters for it. If no flapfinder is specified, a default will be allocated, using the parameters specified for fragment evaluation, below.
Two flapfinders are currently provided:
net.genefront.selectortools.piecemaker.ops.impl.NoEndoPositionCalculator
Performs no selection of flap positions
net.genefront.selectortools.piecemaker.ops.impl.FivePrimeEndoPositionCalculator
Selects one position for a 5' flap, satisfying the following settings, if necessary and possible. Otherwise selects no flap position, resulting in the fragment being discarded in the following step.
These settings specify the fragment filter used for accepting restriction fragments. (This filter can be omitted, but no filtering will be performed, resulting in a very large number of undesired fragments.)
The recommended filter to use here is:
net.genefront.selectortools.piecemaker.ops.impl.DefaultFragmentFilter
The combination selector is responsible for evaluating the possible combinations of restriction reactions, and finding the combination that best satisfies its selection criteria. The following combination selectors are currently available:
net.genefront.selectortools.piecemaker.ops.impl.BaseCoverageCombinationSelector
Finds a combination with the largest number of total ROI bases covered by all fragments.
net.genefront.selectortools.piecemaker.ops.impl.BaseCoverageOverlapCombinationSelector
As above, but a number of bases at each end of a fragment are not considered when calculating the coverage. This results in combinations with fragments with overlapping ends.
net.genefront.selectortools.piecemaker.ops.impl.FullCoverageCombinationSelector
Finds a combination with the largest number of targets for which all ROI bases are covered.
net.genefront.selectortools.piecemaker.ops.impl.FullCoverageOverlapCombinationSelector
As above, but a number of bases at each end of a fragment are not considered when calculating the coverage.
net.genefront.selectortools.piecemaker.ops.impl.OneAcceptedCombinationSelector
Finds a combination with the largest number of targets for which there is at least one accepted fragment.
The fragment set selector is used to select a subset of fragments from a reaction combination. This subset is selected to fulfill the criteria defined by each subset selector. The following subset selectors that are suitable for resequencing applications are currently available:
net.genefront.selectortools.piecemaker.ops.impl.CoverageSubSetSelector
Select a subset of fragment that retains maximum coverage.
net.genefront.selectortools.piecemaker.ops.impl.CoverageOverlapSubSetSelector
Select a subset of fragment that retains maximum coverage, not counting the ends of each fragment.
The following lists the settings for ProbeMaker that are relevant for the selector design application. These settings affect the way the selector probe sequences are assembled based on the selected restriction fragments. For details and other uses of ProbeMaker, refer to the ProbeMaker web site.
Setting the min and max values equal will specify that length to all sequences.
As seen above, there are several places where the same value will go, for example minimum fragment length. To make changing the settings less cumbersome, variables can be used. Variables are defined in the settings file like this:
$variableName1=value1 $variableName2=value2
and can then be used like this:
key1=${variableName1}
key2=${variableName2}Changing the value in one place thus effectively changes it in all places where it is used. This can help make the settings file simpler to use.