| More docs on the ARB website. See also index of helppages. Last update on 27. Jun 2017 .

Main topics:

- ARB: a Short Introduction
- Glossary

Related topics:

- Write to File
- Probe Match

# Potential Probe Targets

- OCCURRENCE
- DESCRIPTION
- SORTING
- NOTES
- EXAMPLES
- WARNINGS
- BUGS

## 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 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 get hitten than allowed.

                                        1000
    quality = groupsize * COL + ----------------------
                                 1000 + (hits in COL)

### 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