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Last update on 25. Nov 2018 .
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Probe Match

OCCURRENCE

ARB_NT/Probes/Match Probes

 

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.

Check the 'Use weighted mismatches' switch to use the custom weights defined via 'EXPERT' button (see ´Probe match (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 '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.

The 'IUPAC' button allows to match multiple probes by specifying a probe containing IUPAC codes (see ´Resolve IUPAC for Probe Match´).

 

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.

See ´Copy and Paste´ for howto paste text into the probe target field.

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

The number of results is limited to 1000000 hits by default. You may change that limit in the expert subwindow.