source: tags/arb_5.1/HELP_SOURCE/oldhelp/probedesign.hlp

#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     probe_param.hlp
SUB     probedesignresult.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 strunk ********
TITLE           Probe Design

OCCURRENCE      ARB_NT/ETC/Probe Design


DESCRIPTION     Searches for potential probe target sites within the sequence
                entries of the corresponding 'PT_SERVER' (not the current)
                database.

                Mark (single or group of) species (ARB_NT <MARK button>;
                        ARB_NT/Species/...) for which probe target sites should
                        be found.

                Choose the 'Probe design' item from the 'ARB_NT/ETC' menu to
                        display the 'PROBE DESIGN' window.

SECTION         PARAMETERS

                (press Probe-Parameter help to get detailed information )

                Select a PT_SERVER:

                       Probe design is not run on your database but on the pt_server's
                       (see 'PT_SERVER What Why and How').
                       To work on a consistent database you should

                          1. re-build the pt_server or

                          2. run arb on the same database as used
                             by the pt_server ($ARBHOME/lib/pts/*.arb)

                Length of output:

                          Clip too long output lists

                Max. non group hits:

                     Maximum number of species, that
                     are not marked but matches a probe

                Max. hairpin bonds:

                     Currently not implemented.

                Min. group hits:

                     Minimum percentage of marked species to match a probe.

                ECOLI-position:

                                        Restricts the target position.
                                        This requires:

                                        1. Your (pt_server) data is aligned.

                                        2. There is a SAI named 'ECOLI' which
                                           includes the reference sequence.

NOTES           The 'PT_SERVER' database ('*.arb' and '*.arb.pt') stored in
                '$ARBHOME/lib/pts' is used for probe target searching not the
                current database.

                The 'PT_SERVER' database has to be updated ('ARB_NT/ETC/Probe
                Admin') if species entries should be considered for probe target
                searching which have been added or modified (sequence symbols)
                later than the date of the most recent 'PT_SERVER' database
                update.

                Probe target searching does not depend on correctly aligned
                sequences and is not affected by any modifications of database
                entries except changes of sequence residues.


EXAMPLES        None


WARNINGS        Take care that only and all species are marked for which a group
                specific probe has to be designed! If the displayed tree is used
                for species marking, consider that species belonging to the
                specificity group but not contained in this tree will remain
                unmarked and treated as non-targets.

                Consequently, useful target sites may be not detected.
                Similarly marked species not related to the target species and
                not contained in the displayed tree will be treated as targets.

BUGS            No bugs known