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Last update on 04. Mar 2022 .
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Multiprobe Calculation

DESCRIPTION  

Finds an optimal probe-triple given a set of probes. Often a group of species cannot be detected by a single oligo-nucleic probe. So several ( normally 3) probes are combined to get a better result. Each probe is labeled with a unique color (see ´Multiprobe results´).

 

NOTES  

WHAT DOES MULTI PROBE DO NOT

It does not generate new probes!

WHAT DOES IT DO

It combines a given set of probes (eg. the results of several probe design processes ).

The MULTI PROBE main window shows two selection list. The upper left one is just used as a temporary clipboard. The upper right shows all probes that will be used in further calculations.

INPUT

As input a list of precomputed probes is expected. Normally you simply use the result from a former probe design session, you transfer the data using save and load.
If you plan to use your probe design to get probes for MULTI PROBE, you should loosen the parameter set:
SET high values for 'Max non group hits' ( +- 200) and low values for 'Min group hits (%)' (+- 30%)

PARAMETERS

PT_SERVER
See ´PT_SERVER: What Why and How´ for more details
Build
select number of probes in target set
Check complement
check also the complement. This should be the default selection, if you are mixing probes with target sequences.
Weight mismatches
If set, minor mismatches and mismatches at the ends of the probe are down weighted.
Max. non group hits
As you can never be sure that your tree is absolutely correct, you allow a few non group hits. If you set this parameter to a too small value, you will not get any or good results.
Min. mismatches for non group
the better your technical assistant the lower the value of this parameter.
Max mismatches for group
Often a small mismatch ( GU instead of GC, or GA instead of TA) does not destabilize a probe.

COMPUTATION

Normally there are too many combinations of probes to be tested. So the program uses a heuristic approach to find a good but not optimal solution. The program never stops unless the user stops the computation by hand pressing the kill button.

RESULT

Read the result help text.
 

NOTES  

You get much better results if all sequences are full sequences. Maybe you should delete all short sequences from the dataset, and create a new pt_server index file.

The pt_server index file and the currently loaded database should be nearly identical.

The program never stops. If you think you cannot wait any longer press kill and inspect the results.

The target group and nothing else should be marked. Be sure that you don't forget species to mark, especially if you are not working with the complete tree.

The buttons at the bottom of the window:

  • 'Compute' calculates possible results
  • 'Open result window' : This button can be chosen to go directly to the result window without calculation(i.e. to load an old result list)

The colors for the probes can be specified in the ARB Properties->Tree:

Color and Fonts