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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.