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

• 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.