source: tags/ms_r16q4/HELP_SOURCE/oldhelp/probe_param.hlp

Last change on this file was 14042, checked in by westram, 9 years ago
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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      probedesign.hlp
5
6#Please insert subtopic references  (line starts with keyword SUB)
7#SUB    pd_spec_param.hlp
8SUB     probedesignresult.hlp
9
10# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
11
12#************* Title of helpfile !! and start of real helpfile ********
13TITLE           Probe Design parameters
14
15OCCURRENCE      ARB_NT/Probes/Design Probes
16
17DESCRIPTION     Allows to select the 'PT_SERVER' and its database, to customize
18                the presentation of the results, define the stringency of target
19                search and physical characteristics of the probes.
20
21                Select the 'PT_SERVER' to use:
22
23                        Probe design is not run on your current database, but on
24                        the database state at the time the PT_SERVER has been
25                        updated (see LINK{pt_server.hlp}).
26
27                        After changing sequence data or species IDs or after
28                        adding new sequences to the database, you need to
29                        update the PT_SERVER to get correct results
30                        (see LINK{probeadmin.hlp}).
31
32                Length of output:
33
34                        Defines the number of probe target proposals to be
35                        displayed in the 'PD RESULT' window (see LINK{probedesignresult.hlp}).
36                        If more probes are found, the result list will be clipped.
37
38                Max. non-group hits:
39
40                        Defines the maximum number of matched species accepted outside of the
41                        group of species that have been marked.
42                        If more species are matched by a probe, the probe gets discarded.
43
44                        This helps not to miss potential target sites in case
45                        that species belonging to the particular specificity
46                        group had been overlooked while marking.
47
48                Max. hairpin bonds:
49
50                        Defines the maximum number of accepted, potential inter- and intraprobe
51                        base pairings.
52
53                        !!! Not implemented !!!
54
55                Min group hits:
56
57                        Defines the minimum fraction (%) of target species (=marked species)
58                        which have to share the target site.
59                        Probe targets matching fewer target species will be discarded.
60
61                        This helps to design multiple probes in case that common
62                        target sites are not present in all species of the
63                        particular specificity group.
64
65                Length of probe:
66
67                        Defines the minimum and maximum length of designed probe targets.
68                        Shorter or longer probe targets will be discarded.
69
70                Temperature:
71
72                        Defines a range of allowed dissociation temperatures (= 4xGC +
73                        2xAU; centigrade) for designed probe targets.
74
75                G+C content:
76
77                        Defines a range of allowed G+C fractions (%) for designed probe targets.
78
79                ECOLI position:
80
81                        Defines a preferred sequence (alignment) region
82                        for the probe target sites.
83
84                        The positions of that region have to be specified
85                        relative to the E.coli molecule (Hint: ARB_EDIT4 displays the
86                        E.coli position of the cursor in its top area).
87
88                        Doing so requires that:
89
90                                1. your data was aligned (when PT_SERVER was updated)
91
92                                2. there is a SAI named 'ECOLI' which
93                                   contains the reference sequence.
94
95                Press the 'EXPERT' button to use individually weighted
96                base pairings (see LINK{pd_spec_param.hlp}).
97
98
99NOTES           Increasing of the 'Max. non group hits' and reducing
100                'Min. group hits (%)' values as well as increasing of the
101                difference of the minimum and maximum values for 'Length of
102                probe', 'Temperature' as well as 'G+C content' reduces the
103                performance (speed) of the program.
104
105                The results will be shown within the 'PD RESULT' window which
106                can be displayed by pressing the 'RESULT' button. The window is
107                automatically displayed when the probe search is completed.
108
109EXAMPLES        None
110
111WARNINGS        None
112
113BUGS            No bugs known
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