| 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

Related topics:

- Probe Parameters
- Potential Probe Targets

# Probe Design

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

## OCCURRENCE

### ARB_NT/ETC/Probe Design

## DESCRIPTION

### Searches for potential probe target sites within the sequence entries of the corresponding 'PT_SERVER' (not the current) database.

### Mark (single or group of) species (ARB_NT <MARK button>; ARB_NT/Species/...) for which probe target sites should be found.

### Choose the 'Probe design' item from the 'ARB_NT/ETC' menu to display the 'PROBE DESIGN' window.

## PARAMETERS

### (press Probe-Parameter help to get detailed information )

### Select a PT_SERVER:

Probe design is not run on your database but on the pt_server's (see 'PT_SERVER What Why and How'). To work on a consistent database you should

1. re-build the pt_server or
2. run arb on the same database as used by the pt_server ($ARBHOME/lib/pts/*.arb)

### Length of output:

Clip too long output lists

### Max. non group hits:

Maximum number of species, that are not marked but matches a probe

### Max. hairpin bonds:

Currently not implemented.

### Min. group hits:

Minimum percentage of marked species to match a probe.

### ECOLI-position:

Restricts the target position. This requires:

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

## NOTES

### The 'PT_SERVER' database ('*.arb' and '*.arb.pt') stored in '$ARBHOME/lib/pts' is used for probe target searching not the current database.

### The 'PT_SERVER' database has to be updated ('ARB_NT/ETC/Probe Admin') if species entries should be considered for probe target searching which have been added or modified (sequence symbols) later than the date of the most recent 'PT_SERVER' database update.

### Probe target searching does not depend on correctly aligned sequences and is not affected by any modifications of database entries except changes of sequence residues.

## EXAMPLES

### None

## WARNINGS

### Take care that only and all species are marked for which a group specific probe has to be designed! If the displayed tree is used for species marking, consider that species belonging to the specificity group but not contained in this tree will remain unmarked and treated as non-targets.

### Consequently, useful target sites may be not detected. Similarly marked species not related to the target species and not contained in the displayed tree will be treated as targets.

## BUGS

### No bugs known