#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    sub.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/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 LINK{pm_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 '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.

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

                The 'IUPAC' button allows to match multiple probes
                by specifying a probe containing IUPAC codes (see LINK{pd_match_iupac.hlp}).

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 LINK{copyNpaste.hlp} 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.