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

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 3.1 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      arb_edit4.hlp
5UP      extended.hlp
6
7#       sub topics:
8SUB     helixsym.hlp
9SUB     toggle_secinfo.hlp
10SUB     e4_options.hlp
11
12# format described in ../help.readme
13
14
15TITLE           Helix
16
17OCCURRENCE      ARB_EDIT4/Edit/Reload Helix
18
19DESCRIPTION     The 'SAI' (see LINK{glossary.hlp}) entry 'HELIX_NR' contains
20                numbering of potential higher order structure elements. The
21                paired 5' and 3' helix halves are indicated by identical
22                numbers. The SAI entry 'HELIX' contains symbols ([<( and )>])
23                indicating positions which usually are base paired. This
24                information is used by the editor to check the sequences for
25                (correct) base pairing. User-defined symbols indicating base pairing and
26                mispairing are shown below the particular sequences.
27
28
29SECTION FORMAT OF HELIX/HELIX_NR:
30
31                When the 'HELIX/HELIX_NR SAI's are analyzed the following steps
32                are performed:
33
34                1. HELIX_NR contains the helix numbering. A helix number
35                   is a number between 0 and 100 optionally followed
36                   by one letter: e.g. 11a, 23g, 0i, 6, 23,
37
38                   A helix number is valid from the position of the
39                   first digit to the position just before the next
40                   helix number.
41
42                        eg.     .........1a.........23b.........
43                        .       .........|||||||||||............
44
45                   The '|' symbols indicate the positions for '1a'
46
47                2. All '<[{(' symbols in HELIX are replaced by '('
48                   All '>]})' symbols in HELIX are replaced by ')'
49
50                        eg.     ...[<<[..]>>].. is the same as ...((((..))))..
51
52                3. For each helix number 'HN' a temporary helix is created
53                   that contains all '()' symbols of the 'SAI HELIX' at
54                   all positions where 'HN' is valid.
55
56                        eg. HELIX_NR    .....1a.....23b.......1a....23b.....
57                            HELIX       .....[<<[...[<[.......]>>]..]>].....
58                            -> 1a       .....((((.............))))..........
59                            -> 23b      ............(((.............))).....
60
61                4.      The (usually) paired positions can simply be defined
62                        by recursively removing the innermost bracket pairs
63                        in the temporary helices:
64
65                        eg. HELIX_NR    .....1a.....23b.......1a....23b.....
66                                HELIX   .....[<<[...[<[.......]>>]..]>].....
67                                Pos     123456789012345678901234567890123456
68                                -> 1a   .....((((.............))))..........
69                                -> 23b  ............(((.............))).....
70                                1a 9-23 ........+-------------+.............
71                                1a 8-24 .......+---------------+............
72                                1a 7-25 ......+-----------------+...........
73                                1a 6-26 .....+-------------------+..........
74                                23b 15-29 .............+------------+.......
75                                23b 14-30 ............+--------------+......
76                                23b 13-31 ...........+----------------+.....
77
78NOTES           After inserting or deleting gaps in the whole alignment (ARB_NT/
79                Sequence/Insert delete columns) the helix information has to be:
80
81                        1. Checked (inserting a '.' between '1' and '2'
82                           destroys the original '12').
83
84                        2. reloaded using 'Reload Helix'
85
86
87EXAMPLES        None
88
89BUGS            No bugs known
Note: See TracBrowser for help on using the repository browser.