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Last update on 04. Dec 2013 .
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Potential Probe Targets

OCCURRENCE

ARB_NT/ETC/Probe Design/PROBE DESIGN/PD RESULT

 

DESCRIPTION

The 'PD RESULT' window is displayed automatically after finishing the probe target searching or manually by pressing the 'RESULT' button of the 'PROBE DESIGN' window.

The parameters defined by in the 'PROBE DESIGN' window are listed in the first line of the display area of the 'PD RESULT' window.

The target and probe sequences are given in the first and last columns of the display area, respectively.

The length of the proposed probe is given in column 2.

Columns 3 and 4 indicate the 5'-positions of the target sites within the alignment and the E.coli sequence, respectively

The number of species targeted (perfectly paired) by the probe is given in column 5.

The G+C contents and predicted dissociation temperatures (4xGC + 2xAT) are listed in columns 6 and 7, respectively.

The numbers of the next columns (from left to right) indicated how many non-target species would be detected by the particular probe if the temperature would be gradually lowered.

!!! The columns do only represent virtual temperature
    shifts and cannot be assigned to degree centigrade!!!

To write the results to an ascii file press the 'SAVE' button to display the 'SELECTION BOX' window.

The 'Auto match' toggle has the same meaning as in ´Probe Match´.

 

SORTING

The program brings the best probes to the front of the list. Best means the product

group_hits * (min. mismatches to non group sp.)

It does not take G+C, temperature or ECOLI position into account. It is up to the user to study the list carefully and choose his candidates. ( In our lab we often found the 20th probe the best ).

 

NOTES

None

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known