| 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 design (Expert)
- What are Marked Species?

# Probe Match

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

## OCCURRENCE

### ARB_NT/ETC/Probe Match

## DESCRIPTION

### Finds and displays all occurrences of a given target and/or probe sequence within any specified 'PT_SERVER' database. The species, targets and additional information are ranked and displayed according to the degree of similarity.

### Select a 'PT_SERVER' from the menu displayed after pressing the 'PT_SERVER' button of the 'PROBE MATCH' window.

### Define whether similar (not perfectly matched) sites should be displayed by pressing the 'Search depth' button and selecting the number of mismatches (1 - 20) from the menu.

### Enable the 'Use weighted mismatches' toggle to use the weights defined via 'EXPERT' button (see ´Probe design (Expert)´).

### Define whether the species which contain the target or probe (or similar) sequence should be marked (see ´What are Marked Species?´) by enabling the 'Mark in database' toggle.

### Define if probe AND target sequence should be searched by enabling the 'Check rev.compl. too' toggle.

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

### Press the 'MATCH' button to perform the search.

### Enabling the 'Auto (match)' toggle will automatically start a probe match whenever the target string is changed. Try it when you design probes.

### The results will be displayed within the display area, ranked according to the degree of similarity between probe string and database entries.

### Brief description of the listed columns:

- name: ID (shortname) of matched species
- fullname: full name of the matched species
- mis: number of mismatches
- N_mis: number of pairings with ambiguous residues (N)
- wmis: mismatch weights
- pos: alignment position of match
- rev: 0=normal match; 1=reverse complement match

### Results from gene PT_servers consist of different columns:

- organism: ID (shortname) of matched organism
- genename: ID (shortname) of matched gene
- mis, N_mis, wmis, rev (same meaning as with normal PT_server)
- pos: position of match in genome sequence
- gpos: position of match in gene sequence

### Sequence sections containing stretches identical or similar to the probe string or its reversed complement are shown between dashes in the last column:

Perfectly matched positions are indicated by double dashes, mismatches by base symbols. The (hybrid destabilizing) quality of mismatches is indicated by upper and lower case letters.

## NOTES

### Unlike the 'ARB_PROBE_DESIGN' tool, the 'ARB_PROBE_MATCH' tool does not depend on the consistency of the current and the 'PT_SERVER' database. Any 'PT_SERVER' database containing homologous or non-homologous, aligned or crude data can be searched for potential probe target matches.

### Please note that all positions returned from PT-Server are in the range [0..N-1]. They differ by 1 from positions in ARB_EDIT4.

## EXAMPLES

### None

## WARNINGS

### None

## BUGS

### The number of results is currently limited to 10000 hits.