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Last update on 04. Dec 2013 .
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Helix

OCCURRENCE

ARB_EDIT/ETC/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/Admin/INS/DEL CHAR) the helix information has to be:

  1. Checked (inserting a '.' between '1' and '2' destroys the original '12').
  2. reloaded by choosing the 'Reload Helix' item of the 'ARB_EDIT/ETC' menu.

 

EXAMPLES

None

 

BUGS

No bugs known