#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	arb.pdf
SUB	mp_params.hlp
SUB	multiproberesults.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		Multiprobe Calculation


DESCRIPTION	Finds an optimal probe-triple given a set of probes.
		Often a group of species cannot be detected by a single
		oligo-nucleic probe. So several ( normally 3) probes are
		combined to get a better result. Each probe is labeled with
		a unique color (see LINK{multiproberesults.hlp}).

NOTES           WHAT DOES MULTI PROBE DO NOT

                     It does not generate new probes!

                WHAT DOES IT DO

                     It combines a given set of probes (eg. the results of
                     several probe design processes ).

		The MULTI PROBE main window shows two selection list. The
		upper left one is just used as a temporary clipboard. The
		upper right shows all probes that will be used in further
		calculations.

        INPUT

                        As input a list of precomputed probes is expected. Normally
        		you simply use the result from a former probe design session,
        		you transfer the data using save and load.

        		If you plan to use your probe design to get probes for
        		MULTI PROBE, you should loosen the parameter set:

        			SET high values for 'Max non group hits' ( +- 200)
        			and low values for 'Min group hits (%)' (+- 30%)


        PARAMETERS

        	PT_SERVER

                        See LINK{pt_server.hlp} for more details

        	Build

                        select number of probes in target set

        	Check complement

                                        check also the complement. This should be
                                        the default selection, if you are mixing probes
                                        with target sequences.

        	Weight mismatches

                                        If set, minor mismatches and mismatches at
                                        the ends of the probe are down weighted.

        	Max. non group hits

                                        As you can never be sure that your tree
                                        is absolutely correct, you allow a few non group hits.
                                        If you set this parameter to a too small value, you
                                        will not get any or good results.

        	Min. mismatches for non group

                                                the better your technical assistant
                                                the lower the value of this parameter.

        	Max mismatches for group

                                                Often a small mismatch ( GU instead
                                                of GC, or GA instead of TA) does not destabilize a probe.


        COMPUTATION

                        Normally there are too many combinations of probes to be tested.
        		So the program uses a heuristic approach to find a good but
        		not optimal solution. The program never stops unless the
        		user stops the computation by hand pressing the kill button.

        RESULT

                        Read the result help text.


NOTES		You get much better results if all sequences are full sequences.
		Maybe you should delete all short sequences from the dataset,
		and create a new pt_server index file.

		The pt_server index file and the currently loaded database
		should be nearly identical.

		The program never stops. If you think you cannot wait any longer
		press kill and inspect the results.

		The target group and nothing else should be marked. Be sure that
		you don't forget species to mark, especially if you are not
		working with the complete tree.

        The buttons at the bottom of the window:

        	- 'Compute' calculates possible results
        	- 'Open result window' : This button can be chosen to go directly
                  to the result window without calculation(i.e. to load an
                  old result list)

        The colors for the probes can be specified in the ARB Properties->Tree:

        	Color and Fonts