source: branches/port5/HELP_SOURCE/oldhelp/probe_param.hlp

Last change on this file was 3614, checked in by westram, 21 years ago
  • corrected links
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 3.6 KB
Line 
1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP      pt_server.hlp
5UP      probedesign.hlp
6
7#Please insert subtopic references  (line starts with keyword SUB)
8#SUB    pd_spec_param.hlp
9SUB     probedesignresult.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 ********
14TITLE           Probe Parameters
15
16OCCURRENCE      ARB_NT/ETC/Probe Design/PROBE DESIGN
17
18DESCRIPTION     Allows to select the 'PT_SERVER' and its database, to customize
19                the presentation of the results, define the stringency of target
20                search and physical characteristics of the probes.
21
22                Select a 'PT_SERVER':
23
24                        Select the appropriate 'PT_SERVER' from the menu
25                        displayed after pressing the button below the
26                        'PT_SERVER' prompt. The 'PT_SERVER' database (*.arb)
27                        has to be consistent with the current. (see 'Main
28                        Topics': 'Probe Design'; 'PT_SERVER What Why and How')
29
30                Customize output of results:
31
32                        Type the number of probe target proposals to be
33                        displayed in the 'PD RESULT' window by typing it to the
34                        'Length of output' subwindow.
35
36                Define number of accepted non-targets:
37
38                        Type the number of non-target species which you would
39                        accept to be detected by the probe to the 'Max. non
40                        group hits' subwindow.
41
42                        This helps not to miss potential target sites in case
43                        that species belonging to the particular specificity
44                        group had been overlooked while marking (see: 'Main
45                        Topics': 'Probe Design').
46
47                Define number of accepted inter- and intraprobe base pairings:
48
49                        Type the number of potential base pairings within or
50                        between probe molecules.
51                        !!! Not yet implemented !!!
52
53                Define minimum number of target species:
54
55                        Type the fraction (%) of marked species which have to
56                        share the target site to the 'Min. group hits (%)
57                        subwindow.
58
59                        This helps to design multiple probes in case that common
60                        target sites are not present in all species of the
61                        particular specificity group.
62
63                Define length of the probe:
64
65                        Type minimum and maximum number of nucleotides to the
66                        corresponding 'Length of probe' subwindows to define
67                        probe length.
68
69                Define dissociation temperature:
70
71                        A range of allowed dissociation temperatures (= 4xGC +
72                        2xAU; centigrade) can be defined by typing minimum and
73                        maximum values to the corresponding subwindows.
74
75                Define the G+C content:
76
77                        A range of allowed G+C fractions (%) can be defined by
78                        typing minimum and maximum values to the corresponding
79                        subwindows.
80
81                Define target region:
82
83                        A preferred sequence (alignment) region can be defined
84                        for the probe target sites by typing the nucleotide
85                        numbers of the homologous positions within the E. coli
86                        molecule.
87
88                        This requires:
89
90                                1. Your (pt_server) data is aligned.
91
92                                2. There is a SAI named 'ECOLI' which
93                                   includes the reference sequence.
94
95                Press the 'EXPERT' button to display the 'PD SPECIAL' window if
96                        base pairings should be individually weighted (see LINK{pd_spec_param.hlp}).
97
98                Press the 'GO' button to start the calculations.
99
100
101NOTES           Increasing of the 'Max. non group hits' and reducing
102                'Min. group hits (%)' values as well as increasing of the
103                difference of the minimum and maximum values for 'Length of
104                probe', 'Temperature' as well as 'G+C content' reduces the
105                performance (speed) of the program.
106
107                The results will be shown within the 'PD RESULT' window which
108                can be displayed by pressing the 'RESULT' button. The window is
109                automatically displayed when the probe search is completed.
110
111EXAMPLES        None
112
113WARNINGS        None
114
115BUGS            No bugs known
Note: See TracBrowser for help on using the repository browser.