1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
|
#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 (red, green and blue (and mixes of these)).
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
|
