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Main topics: ARB: a Short Introduction Glossary How to start ARB_EDIT4 | Related topics: Define Helix Symbols Toggle secondary info for SAI ARB_EDIT4 Options
# Helix OCCURRENCE DESCRIPTION FORMAT OF HELIX/HELIX_NR: NOTES EXAMPLES BUGS ## 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:
3. ### When the 'HELIX/HELIX_NR SAI's are analyzed the following steps are performed: 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' All '<[{(' symbols in HELIX are replaced by '(' All '>]})' symbols in HELIX are replaced by ')' eg. ...[<<[..]>>].. is the same as ...((((..)))).. 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: Checked (inserting a '.' between '1' and '2' destroys the original '12'). reloaded using 'Reload Helix'
## EXAMPLES
### None
## BUGS
### No bugs known