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Last update on 25. Nov 2018 .
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Helix

OCCURRENCE

ARB_EDIT4/Edit/Reload Helix

 

DESCRIPTION

The 'SAI' (see ´Glossary´) 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.

 

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