#Please insert up references in the next lines (line starts with keyword UP)
UP	arb.hlp
UP	glossary.hlp
UP	pt_server.hlp

#Please insert subtopic references  (line starts with keyword SUB)
#SUB	pd_spec_param.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE		Probe Match

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
		LINK{pd_spec_param.hlp}).

		Define whether the species which contain the target or
		probe (or similar) sequence should be marked (see
		LINK{mark.hlp}) 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 LINK{pd_spec_param.hlp}).

		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: short name of the 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: short name of the matched organism
                  - genename: short name of the 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.

#		To write the results to an ascii file press the 'SAVE'
#		button to display the 'SELECTION BOX' window.


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.
