source: branches/lib/HELP_SOURCE/source/primer_new.hlp

Last change on this file was 19575, checked in by westram, 3 weeks ago
  • reintegrates 'help' into 'trunk'
    • preformatted text gets checked for width now (to enforce it fits into the arb help window).
    • fixed help following these checks, using the following steps:
      • ignore problems in foreign documentation.
      • increase default help window width.
      • introduce control comments to
        • accept oversized preformatted sections.
        • enforce preformatted style for whole sections.
        • simply define single-line preformatted sections
          Used intensive for definition of internal script languages.
    • fixed several non-related problems found in documentation.
    • minor layout changes for HTML version of arb help (more compacted; highlight anchored/all sections).
    • refactor system interface (GUI version) and use it from help module.
  • adds: log:branches/help@19532:19574
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 3.5 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6SUB     iupac-codes.hlp
7
8# format described in ../help.readme
9
10
11TITLE           Design Primers
12
13OCCURRENCE      ARB_NT/Probes/Design Primers
14
15DESCRIPTION     Searches for primer pairs
16                within the given physical and biological ranges
17
18                       1. select a species (ARB_NT <INFO button>)
19                       2. open 'PRIMER DESIGN' window
20                       3. specify search parameters
21                       4. press 'GO' (will open LINK{primer_result.hlp}).
22
23                INIT FROM SPECIES/GENE
24
25                     This initializes the values left and right position and
26                     the primer distance with (hopefully) reasonable defaults.
27
28SECTION         Search parameters
29
30                  Left/right position
31
32                    specifies the ranges (where the primer shall reside) using
33                    a START position and a given NUMBER OF BASES.
34
35                    The actual sequence data of the currently selected species
36                    is examined and the end position of the primer range is
37                    set dynamically, such that the range contains the specified
38                    number of bases.
39
40                  Primer length
41
42                    Specifies a lower and upper limit for the number of bases the
43                    reported primers shall contain.
44
45                  Primer distance
46
47                    Specifies the minimum and maximum wanted
48                    distance (in number of bases) between the
49                    left and right primer of the reported primer pairs.
50                    Optional parameters (ignored if 0).
51
52                  G+C ratio / temperature
53
54                    Specifies minima and maxima for G+C-ratio and temperature of
55                    the reported primers.
56
57                  Min. dist to next match of primer
58
59                    If a value above zero is specified, the search accepts
60                    primers matching at additional positions, if the distance
61                    betweeen the selected position and additional positions is
62                    greater than the specified value.
63
64                    A value of zero or below forces all primers to be well-defined (i.e.
65                    to match only once).
66
67                    Example:
68
69                             primerposition   100
70                             min.dist          50
71                             2nd occurrence    30 => distance 70 => primer remains in list
72                             3rd occurrence   140 => distance 40 => primer is removed from list
73
74                  Expand IUPAC codes
75
76                    If option is checked, all possibilities of IUPAC codes are permutated
77                    when testing for primer matches.
78
79                    When unchecked, primers containing IUPAC codes will not be considered.
80
81                  Max. number of results
82
83                    Limits the number of reported results.
84
85                  G+C- / temperature-factor
86
87                    Allows to weight the impact of G+C vs. temperature while scoring
88                    the reported results.
89
90
91
92NOTES           all specified positions are from range [0 .. N-1], i.e. when you use a position
93                from EDIT4, you need to subtract 1
94
95SECTION         WRITTEN BY
96
97                Wolfram Foerster 2001
98
99EXAMPLES        None
100
101WARNINGS        ARB will crash if you use Primer Design without taking care
102                about the estimated memory needed (lower right corner).
103
104BUGS            No bugs known
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