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Last update on 04. Mar 2022 .
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Potential Probe Targets

OCCURRENCE  

ARB_NT/Probes/Design Probes/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 few lines of the 'PD RESULT' window.

Description of single display columns:

Column          contains
Target          the target sequence of the designed probe
le              length of designed probe
apos            absolute 5'-position of the target sites
                (most often targeted position)
ecol            ecoli-relative position
qual            a probe quality indicator (see below)
grps            groupsize (number of perfect hits in target-species)
G+C             G+C content
temp            predicted dissociation temperature (4GC+2AT)
Probe           the designed probe sequence

The numbers of the next columns (from left to right) indicates how many non-target species would be detected by this probe if the temperature would be gradually lowered ('_' means no hits).

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 probes are sorted by quality. The quality tries to reflect how good each probe separates between target- and non-target group.

Therefore it detects the column COL in the decrease-temparature-list, where more than twice as much non-target species would get hitten, than mishits (i.e. non-group hits) were encountered by matching the probe.

Using that column the quality is calculated using the formula

                                    1000
quality = groupsize * COL + ------------------
                             1000 + hits[COL]
where:
  • COL is in range 0 .. 19
  • mishits = probehits - groupsize
  • probehits = number of hits reported by probe match (zero mismatches)
  • COL is lowest column where: hits[COL] > 2*mishits
  • if no column matches the criterion above, COL=19 is used

Probes with equal qualities are sorted by absolute position and then alphabetically. It does not take G+C content, 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 was the best.

 

NOTES  

None

 

EXAMPLES  

None

 

WARNINGS  

None

 

BUGS  

No bugs known