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 data base.
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: Name of sequences or name of groups.
Second C. Protection level and subtype of sequence.
Last c. Sequence and secondary structure and more.
Cursor:
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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.
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These 3 positions and the IUPAC-display refer to the position
RIGHT of the cursor.
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Position counting now starts with 1 (too many people were
confused about position counting starting at position 0).
Moving entries:
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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.
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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 everything you did.
Jump:
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If you selected a species in any other ARB component
(i.e. in the Tree or in the Search Hitlist), you can
jump to the selected species using this button.
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In general the editor will automatically jump to the
selected species, unless the species is in a folded group.
In this case all necessary groups will be unfolded.
Get:
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If the species is already in the editor 'Get' does the
same as 'Jump'. If the species is NOT loaded in the editor
it will be inserted into the group 'More Sequences'.
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If you like to load several species into the editor, mark
those species and use 'ARB_EDIT4/Edit/Load marked species'
Editing:
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Protection:
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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).
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Note: There are two global protection levels: one in
edit-mode and another one in align-mode.
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Modes:
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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.
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Align-mode:
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Only gap symbols can be inserted ('-', '.' or
'Spc' key) or deleted ('Del' or 'Backspace' key)
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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.
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Edit-mode:
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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.
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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.
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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.
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Repeat editing functions:
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Key mapping:
Nucleotide (amino acid) and gap symbols can be assigned
to any of the letter and symbol keys by using the 'Key
Mapping' facility ('Properties' menu).
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Moving nucleotide (amino acid) symbols:
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Other keys:
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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.
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CTRL+UP/DOWN
Like Ctrl-Left/Right, but vertical.
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HOME/END
Jumps to the start/end of sequence.
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CTRL+HOME/END
Jumps to the first/last sequence.
Messages:
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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.
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You can press one of the small buttons at the left side of this
text window:
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press the small lens to see more errors
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press the small X to get rid of all errors
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