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

#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      glossary.hlp
UP      arb_edit4.hlp
UP      extended.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB     helixsym.hlp
SUB     toggle_secinfo.hlp
SUB     e4_options.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 ********
TITLE           Helix

OCCURRENCE      ARB_EDIT4/Edit/Reload Helix

DESCRIPTION     The 'SAI' (see LINK{glossary.hlp}) entry 'HELIX_NR' contains
                numbering of potential higher order structure elements. The
                paired 5' and 3' helix halves are indicated by identical
                numbers. The SAI entry 'HELIX' contains symbols ([<( and )>])
                indicating positions which usually are base paired. This
                information is used by the editor to check the sequences for
                (correct) base pairing. User-defined symbols indicating base pairing and
                mispairing are shown below the particular sequences.


SECTION FORMAT OF HELIX/HELIX_NR:

                When the 'HELIX/HELIX_NR SAI's are analyzed the following steps
                are performed:

                1. HELIX_NR contains the helix numbering. A helix number
                   is a number between 0 and 100 optionally followed
                   by one letter: e.g. 11a, 23g, 0i, 6, 23,

                   A helix number is valid from the position of the
                   first digit to the position just before the next
                   helix number.

                        eg.     .........1a.........23b.........
                        .       .........|||||||||||............

                   The '|' symbols indicate the positions for '1a'

                2. All '<[{(' symbols in HELIX are replaced by '('
                   All '>]})' symbols in HELIX are replaced by ')'

                        eg.     ...[<<[..]>>].. is the same as ...((((..))))..

                3. For each helix number 'HN' a temporary helix is created
                   that contains all '()' symbols of the 'SAI HELIX' at
                   all positions where 'HN' is valid.

                        eg. HELIX_NR    .....1a.....23b.......1a....23b.....
                            HELIX       .....[<<[...[<[.......]>>]..]>].....
                            -> 1a       .....((((.............))))..........
                            -> 23b      ............(((.............))).....

                4.      The (usually) paired positions can simply be defined
                        by recursively removing the innermost bracket pairs
                        in the temporary helices:

                        eg. HELIX_NR    .....1a.....23b.......1a....23b.....
                                HELIX   .....[<<[...[<[.......]>>]..]>].....
                                Pos     123456789012345678901234567890123456
                                -> 1a   .....((((.............))))..........
                                -> 23b  ............(((.............))).....
                                1a 9-23 ........+-------------+.............
                                1a 8-24 .......+---------------+............
                                1a 7-25 ......+-----------------+...........
                                1a 6-26 .....+-------------------+..........
                                23b 15-29 .............+------------+.......
                                23b 14-30 ............+--------------+......
                                23b 13-31 ...........+----------------+.....

NOTES           After inserting or deleting gaps in the whole alignment (ARB_NT/
                Sequence/Insert delete columns) the helix information has to be:

                        1. Checked (inserting a '.' between '1' and '2'
                           destroys the original '12').

                        2. reloaded using 'Reload Helix'


EXAMPLES        None

BUGS            No bugs known