Alignment editor
Introduction
The Alignment Editor plugin allows viewing of protein sequences,
coloring of residues by some property, and change of alignments.
The user may either select an existing alignment, or a set of chains.
Saving of currently shown alignment uses a PIR-parser plugin.
The sequences shown in the alignment can be re-aligned manually or
by calling the Malign plugin. All modifications happen through
moving the gaps.
Numbering, merge operations etc. are based on the first shown sequence.
The order of sequences in the alignment can be changed. More than one alignment
editor may be active simultaneously.
The window is divided into four sections.:
- Top-left title section shows the name of the currently shown
alignment and has no other functionality.
- Left section shows name for each sequence
and the selection status for each row (X selected, O unselected).
- Top section shows numbering for the first sequence
and the selection status for each column (X selected, O unselected).
- The main section shows the alignment itself. This is the only section
that can be scrolled, although top and left sections will scroll accordingly.
Basic operations
Mouse:
- Over left section:
- Left Button: Toggle selection state for the row.
- Drag Left or Middle Button: Reorder the sequences
- Shift + Middle Button: Create new alignment, which does not have the pointed row.
(i.e. remove sequence from the alignment).
- Rigth Button: Show percentage identity between clicked row and first sequence.
- Over top section:
- Left Button: Toggle selection state for the column. Initializes Range-selection.
- Shift + Left Button: Expand Range-selection.
- Middle Button: Insert column of gaps at pointed location.
- Shift + Middle Button: Remove column. Will also remove columns that contain
amino acids. Won't change the chains, just the alignment. This function is meant
for dropping overhangs from the beginning and end of the alignment.
- Over main section:
- Left Button: Toggle selection of the amino acid.
- Middle Button: If last column does not have gap at pointed row, append column of gaps.
Then shift in pointed sequence each character [pointed,last) to right one column.
(i.e. insert a gap to pointed position. )
- Rigth Button: Show property menu for the amino acid.
- Drag Gap with Left Button: Move single Gap to new location (on the same row).
- Drag Gap with Middle Button: Move whole gap (consecutive
gaps) to new location (on the same row).
Menus
- File
- Seqs: Select sequences from Bodil and create new Alignment object.
- Add Seqs: Create new Alignment object from current
alignment and additional sequences in Bodil.
- Merge: Select alignment, which has same first chain object
as in the current one. Create new combined alignment, using
the common sequence as reference. Gapped regions in common
sequence will not be aligned. Incomplete sequences
(e.g. alignment from iterative superimposition) should now
merge correctly with each other, adding gap columns to missing
positions.
- Combine: Select alignment which has identical first
sequence as in the current one. Create new combined alignment,
using the common sequences as reference. Both common sequences
occur in the new alignment. Gapped regions in common sequences
will not be aligned.
- Ali: Select and show alignment from Bodil.
- Save: Save current alignment to PIR format.
- Close: Set current alignment to none.
- Print Fat: Print alignment, using black text on colored backgroud, as in the window.
- Print Slim: Print alignment, using colored text on white backgroud.
- Print Boxed: Print alignment, using black text on white backgroud and enclose each selected
amino acid in a rectangle.
- Exit: Close plugin
- Model
- If environment variable HOMODGE is set to absolute path of
binary of program HOMODGE, entry Homodge appears. This entry
will write out two first lines of the of the alignment and the
structure of the first sequence. Then, program HOMODGE is
executed, and the resulting model is read into Bodil.
- Select
- ConservedN: Ask N, then select each residue, that
occurs at least in N rows in its column.
- SubSequence: Ask for sequence, then select each
residue that is part of such sequence fragment. A '.'
matches any character, and '-' matches a single gap.
- Range
- Select: select each amino acid in the currently
selected Range.
- Remove: remove columns of the currently selected
Range from the Alignment.
- ReNumber: Ask new starting residue-number for each
sub-sequence in the currently selected Range. Then
renumber each sub-sequence consecutively from given start
values. No consistency checks.
- Add SSE: create secondary structure element for
Range in the first sequence. Works only, if the
residues in range do not already have SSE.
- Color
- Selected: Choose new color for currently selected
amino acids.
- Conserved: Color each column, where at least N-1
rows have the same amino acid.
- ConservedN: Ask N, then color each column, where at
least N rows have the same amino acid.
- By Property: Show the PropertyColor dialog.
- By Distance: Color each column by average Ca-Ca
distance using Blue-to-Red ( 0.0 to 6.0Å ) map.
White for gaps and unpositioned acids.
- Help: Show this help
Toolbar
From left to right
- Select sequences from Bodil and create new Alignment object.
- Select and show alignment from Bodil.
- Select and delete alignment from Bodil.
- Choose new color for currently selected amino acids.
- Show the PropertyColor dialog.
- Color each column, where at least N-1 rows have the same amino acid.
- Change font.
- Call Malign plugin to do a sequence alignment. Only the first continuous
range of selected columns will be sent to Malign, if any columns are selected,
otherwise full aligment occurs.
The PropertyColor dialog
The dialog has a drop-down box of defined amino acid properties. For each property, a value exists for every
amino acid and a Colormap is defined. Selecting a property will use the Colormap and values to create a color
for each amino acid type. They are shown in the dialog. Clicking Apply will use that color for each amino acid
in the alignment. Clicking OK also applies the color and closes the dialog. Cancel will close the dialog without
applying color.
Configuration file entries
Section Key Valuetype
Description
Directories Icons dirname
location for Icon.
SEDI2 Icon filename
pixmap Icon for minimized window.
SE2_Colormaps SE2_property colormap
the
colormap file for each AA-property
SEDI2 PrintSSE boolean
add secondary structure
indicators into the printed version.
SEDI2 Font fontname
default font
SEDI2 SimpleRegExp boolean
use simple syntax
('.' is any character) for SubSequence selection. Complex version
uses regular expressions.
SEDI2 DistanceColorMap colormap
the colormap used to
color residues according to the accuracy of superimposition.
SEDI2 DistanceCutoffMin float
residues closer
than cutoff use the low end of color map.
SEDI2 DistanceCutoffMax float
residues more
distant than cutoff use the top end of color map.
Contents