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Last update on 25. Nov 2018 .
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ARB_EDIT4 - Sequence primary and secondary structure editor

OCCURRENCE

ARB_NT/Sequence/Edit marked sequences

 

DESCRIPTION

The editor allows you to view and modify the sequences of 'marked species' or 'a selection of species' and 'SAI' (sequence associated information) stored in the database. Potential secondary structure is automatically checked and the information can be displayed with the primary structure. In addition, an online column statistic may help you find sequence and alignment errors.

The editor permanently communicates with the database and other ARB tools. Every change made by the editor is immediately exported to the database. All sequence changes made by other ARB tools are exported to the editor every 5 seconds.

Multiple editors can be used synchronously.

Display:

First Column:   Species ID or group name.
Second C.       Protection level and subtype of sequence.
Last c.         Sequence and secondary structure and more.

Cursor:

The cursor can be moved using the mouse or the arrow keys. The current cursor positions with respect to the alignment and the E. coli sequence (there has to be an 'SAI' entry: ECOLI) are indicated after the 'Position' and 'E.coli' prompts in the upper part of the 'ARB_EDIT4' window.
These 3 positions and the IUPAC-display refer to the position RIGHT of the cursor.
'Position' counts from 1 to "alignment length".
The 'Ecoli'- and 'Base'-position count from zero to "number of bases".
  • Zero means your cursor is left of the first base (and not AT the first base).
  • X means your cursor is AT or BEHIND base number X (but in front of base number X+1)

By changing the value of one of these fields, the cursor will be repositioned. Negative values are possible - in that case the position will be calculated from the right end (e.g. -1 in 'Base' field means 'position onto base')

Moving entries:

To move an individual entry, position the cursor on the name, keep the left mouse button pressed, move the entry to the desired position, and release the button.
Any entry can be fixed (keeps its position while scrolling vertically) at the top of the editing area by moving it somewhere above the double line (=top area).

Undo/Redo:

This undoes/redoes all performed database changes (see ´Undo/Redo´).

Editing:

Protection:
To perform editing, the protection level of the particular entry ('EDIT/Set protection of selected species') has to be set below or equal the global protection level (use the 'Protect' button on the menuboard).
Note: There are two global protection levels: one in edit-mode and another one in align-mode.
Modes:
ARB_EDIT4 supports 2 modes: Align-mode and Edit-mode. To toggle between these two modes use the 'Align/Edit' button on the menuboard or press CTRL-E.
Align-mode:
Only gap symbols can be inserted ('-', '.' or 'Spc' key) or deleted ('Del' or 'Backspace' key)
Sequence data cannot be modified - it only can be checked in this mode. Sequence check is performed by typing nucleotide (amino acid) symbols. Discrepancies between typed and existing symbols are indicated by beeping.
Edit-mode:
Edit-mode is divided into two submodes: Insert-mode and Replace-mode. Toggle between these submodes with the 'Insert/Replace' button on the menuboard or with CTRL-I.
In Replace-mode inserted Nucleotides/gaps overwrite existing Nucleotides/gaps. In Insert-mode inserted Nucleotides/gaps do not overwrite, instead the whole sequence is shifted.
Direction:
ARB_EDIT4 should perform any editing function into both directions - forward and backward. To toggle the editing direction use the "5'->3'" button on the menuboard.
Repeat editing functions:
Nearly every editing function can be performed repeatedly by typing some digits before you perform the editing function.
Example:  '9-' inserts nine '-'
If you need to insert digits, use the toggle in 'Properties/Options'.
Key mapping:
Nucleotide (amino acid) and gap symbols can be assigned to any of the letter and symbol keys using 'Properties/Key mappings'.
Moving nucleotide (amino acid) symbols:
SHIFT + LEFT/RIGHT
Push or pull a coherent sequence stretch next to the cursor.
ALT + LEFT/RIGHT
Move a single nucleotide (amino acid) symbol.
If you move your cursor towards a gap, the next nucleotide (amino acid) symbol in movement direction is fetched and moved to the actual position.
If you move your cursor towards a nucleotide (amino acid) symbol, it will jump aside the next nucleotide (amino acid) symbol.
Alternate keys are: CTRL-O and CTRL-P
Change gap type
Consecutive runs of gaps can be set to
CTRL-'-'         minus sign (normal gaps)
CTRL-'.'         dots (recommended at both sequence ends)
CTRL-SPACE       toggles between both gap types
These gap types have different meanings:
'-'        is only used for aligning
'.'        marks potentially missing bases
Other keys:
CTRL+LEFT/RIGHT
Jumps to the start of the next gap-region or non-gap-region. You may configure whether it always jumps over gap-regions.
CTRL+UP/DOWN
Like CTRL-LEFT/RIGHT, but vertical.
HOME/END
Jumps to the start/end of sequence.
CTRL+HOME/END
Jumps to the first/last sequence.
ENTER
Fold/unfold group
ALT+UP/DOWN
Jump to previous/next group consensus
CTRL-A
Call Aligner with current settings (see ´The integrated aligners´).
CTRL-D
Toggle "view differences" mode (see ´View differences to selected´).
CTRL-E
Toggle EDIT/ALIGN mode (see above).
CTRL-I
Toggle INSERT/REPLACE mode (see above).
CTRL-J
Jump to opposite helix position.
CTRL-L
Move cursor into view and refresh display.
CTRL-M
Toggle mark of species/group.
CTRL-R
Shared key:
CTRL-S
Repeat last search (see ´Search and highlight sequence patterns´).

Messages:

Many (less serious) errors will not be announced by a popup window. Instead they appear at the small text window in the upper-right corner of the editor window.
You can press one of the small buttons at the left side of this text window:
  • press the small lens to see more errors
  • press the small X to get rid of all errors

 

EXAMPLES

None

 

NOTES

You may use the META key instead of ALT (especially if there is no ALT key :)

 

WARNINGS

The key mappings may conflict with some window managers (eg. olvwm). Disable the CTRL-LEFT/RIGHT keys of the window manager.

If you perform major database modifications such as

  • adding new SAIs

you have to QUIT and restart the editor.

 

BUGS

  • sometimes the editor crashes after aligning
  • some update problems (please report system and circumstances) (workaround: resize the editor window)