source: branches/tree/HELP_SOURCE/source/multiprobe.hlp

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1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP      pt_server.hlp
5
6#Please insert subtopic references  (line starts with keyword SUB)
7SUB     arb.pdf
8SUB     mp_params.hlp
9SUB     multiproberesults.hlp
10
11# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
12
13#************* Title of helpfile !! and start of real helpfile strunk ********
14TITLE           Multiprobe Calculation
15
16
17DESCRIPTION     Finds an optimal probe-triple given a set of probes.
18                Often a group of species cannot be detected by a single
19                oligo-nucleic probe. So several ( normally 3) probes are
20                combined to get a better result. Each probe is labeled with
21                a unique color (see LINK{multiproberesults.hlp}).
22
23NOTES           WHAT DOES MULTI PROBE DO NOT
24
25                     It does not generate new probes!
26
27                WHAT DOES IT DO
28
29                     It combines a given set of probes (eg. the results of
30                     several probe design processes ).
31
32                The MULTI PROBE main window shows two selection list. The
33                upper left one is just used as a temporary clipboard. The
34                upper right shows all probes that will be used in further
35                calculations.
36
37        INPUT
38
39                        As input a list of precomputed probes is expected. Normally
40                        you simply use the result from a former probe design session,
41                        you transfer the data using save and load.
42
43                        If you plan to use your probe design to get probes for
44                        MULTI PROBE, you should loosen the parameter set:
45
46                                SET high values for 'Max non group hits' ( +- 200)
47                                and low values for 'Min group hits (%)' (+- 30%)
48
49
50        PARAMETERS
51
52                PT_SERVER
53
54                        See LINK{pt_server.hlp} for more details
55
56                Build
57
58                        select number of probes in target set
59
60                Check complement
61
62                                        check also the complement. This should be
63                                        the default selection, if you are mixing probes
64                                        with target sequences.
65
66                Weight mismatches
67
68                                        If set, minor mismatches and mismatches at
69                                        the ends of the probe are down weighted.
70
71                Max. non group hits
72
73                                        As you can never be sure that your tree
74                                        is absolutely correct, you allow a few non group hits.
75                                        If you set this parameter to a too small value, you
76                                        will not get any or good results.
77
78                Min. mismatches for non group
79
80                                                the better your technical assistant
81                                                the lower the value of this parameter.
82
83                Max mismatches for group
84
85                                                Often a small mismatch ( GU instead
86                                                of GC, or GA instead of TA) does not destabilize a probe.
87
88
89        COMPUTATION
90
91                        Normally there are too many combinations of probes to be tested.
92                        So the program uses a heuristic approach to find a good but
93                        not optimal solution. The program never stops unless the
94                        user stops the computation by hand pressing the kill button.
95
96        RESULT
97
98                        Read the result help text.
99
100
101NOTES           You get much better results if all sequences are full sequences.
102                Maybe you should delete all short sequences from the dataset,
103                and create a new pt_server index file.
104
105                The pt_server index file and the currently loaded database
106                should be nearly identical.
107
108                The program never stops. If you think you cannot wait any longer
109                press kill and inspect the results.
110
111                The target group and nothing else should be marked. Be sure that
112                you don't forget species to mark, especially if you are not
113                working with the complete tree.
114
115        The buttons at the bottom of the window:
116
117                - 'Compute' calculates possible results
118                - 'Open result window' : This button can be chosen to go directly
119                  to the result window without calculation(i.e. to load an
120                  old result list)
121
122        The colors for the probes can be specified in the ARB Properties->Tree:
123
124                Color and Fonts
125
126
127
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