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

Main topics:

- ARB: a Short Introduction
- Glossary
- PT_SERVER: What Why and How
- Probe Design

Related topics:

- Potential Probe Targets
- Probe design (Expert)

# Probe Parameters

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

## OCCURRENCE

### ARB_NT/ETC/Probe Design/PROBE DESIGN

## 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 a 'PT_SERVER':

Select the appropriate 'PT_SERVER' from the menu displayed after pressing the button below the 'PT_SERVER' prompt. The 'PT_SERVER' database (*.arb) has to be consistent with the current. (see 'Main Topics': 'Probe Design'; 'PT_SERVER What Why and How')

### Customize output of results:

Type the number of probe target proposals to be displayed in the 'PD RESULT' window by typing it to the 'Length of output' subwindow.

### Define number of accepted non-targets:

Type the number of non-target species which you would accept to be detected by the probe to the 'Max. non group hits' subwindow.
This helps not to miss potential target sites in case that species belonging to the particular specificity group had been overlooked while marking (see: 'Main Topics': 'Probe Design').

### Define number of accepted inter- and intraprobe base pairings:

Type the number of potential base pairings within or between probe molecules. !!! Not yet implemented !!!

### Define minimum number of target species:

Type the fraction (%) of marked species which have to share the target site to the 'Min. group hits (%) subwindow.
This helps to design multiple probes in case that common target sites are not present in all species of the particular specificity group.

### Define length of the probe:

Type minimum and maximum number of nucleotides to the corresponding 'Length of probe' subwindows to define probe length.

### Define dissociation temperature:

A range of allowed dissociation temperatures (= 4xGC + 2xAU; centigrade) can be defined by typing minimum and maximum values to the corresponding subwindows.

### Define the G+C content:

A range of allowed G+C fractions (%) can be defined by typing minimum and maximum values to the corresponding subwindows.

### Define target region:

A preferred sequence (alignment) region can be defined for the probe target sites by typing the nucleotide numbers of the homologous positions within the E. coli molecule.
This requires:

1. Your (pt_server) data is aligned.
2. There is a SAI named 'ECOLI' which includes the reference sequence.

### Press the 'EXPERT' button to display the 'PD SPECIAL' window if base pairings should be individually weighted (see ´Probe design (Expert)´).

### Press the 'GO' button to start the calculations.

## 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