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Last update on 25. Nov 2018 .
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Probe Design parameters

OCCURRENCE

ARB_NT/Probes/Design Probes

 

DESCRIPTION

Allows to select the 'PT_SERVER' and its database, to customize the presentation of the results, define the stringency of target search and physical characteristics of the probes.

Select the 'PT_SERVER' to use:

Probe design is not run on your current database, but on the database state at the time the PT_SERVER has been updated (see ´PT_SERVER: What Why and How´).
After changing sequence data or species IDs or after adding new sequences to the database, you need to update the PT_SERVER to get correct results (see ´PT_SERVER Administration´).

Length of output:

Defines the number of probe target proposals to be displayed in the 'PD RESULT' window (see ´Potential Probe Targets´). If more probes are found, the result list will be clipped.

Max. non-group hits:

Defines the maximum number of matched species accepted outside of the group of species that have been marked. If more species are matched by a probe, the probe gets discarded.
This helps not to miss potential target sites in case that species belonging to the particular specificity group had been overlooked while marking.

Max. hairpin bonds:

Defines the maximum number of accepted, potential inter- and intraprobe base pairings.
!!! Not implemented !!!

Min group hits:

Defines the minimum fraction (%) of target species (=marked species) which have to share the target site. Probe targets matching fewer target species will be discarded.
This helps to design multiple probes in case that common target sites are not present in all species of the particular specificity group.

Length of probe:

Defines the minimum and maximum length of designed probe targets. Shorter or longer probe targets will be discarded.

Temperature:

Defines a range of allowed dissociation temperatures (= 4xGC + 2xAU; centigrade) for designed probe targets.

G+C content:

Defines a range of allowed G+C fractions (%) for designed probe targets.

ECOLI position:

Defines a preferred sequence (alignment) region for the probe target sites.
The positions of that region have to be specified relative to the E.coli molecule (Hint: ARB_EDIT4 displays the E.coli position of the cursor in its top area).
Doing so requires that:
  1. your data was aligned (when PT_SERVER was updated)
  2. there is a SAI named 'ECOLI' which contains the reference sequence.

Press the 'EXPERT' button to use individually weighted base pairings (see ´Probe design (Expert)´).

 

NOTES

Increasing of the 'Max. non group hits' and reducing 'Min. group hits (%)' values as well as increasing of the difference of the minimum and maximum values for 'Length of probe', 'Temperature' as well as 'G+C content' reduces the performance (speed) of the program.

The results will be shown within the 'PD RESULT' window which can be displayed by pressing the 'RESULT' button. The window is automatically displayed when the probe search is completed.

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known