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9.5 Alignment Editor
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[ Edit | Save/Print/Del | Add Comment | Trees | Color | Shade/Box | View Options | Gaps | Search | Selections | Selections | Consensus ]

The default position for the alignment editor is at the bottom of the graphical user interface. If you have made an alignment and you cannot see the alignment you can select Window/Alignments ( See Window Menu section of this manual ) and it will be displayed.

ICM has an easy to use editor for pairwise and multiple alignments. ICM alignment editor is robust and always protects the integrity of your alignment by protecting you from making unintended changes in the alignment.

NOTE: To increase or decrease the size of the font in the Alignment Editor press the CTRL key and the '+' or '-' keys.

9.5.1 Edit an Alignment


To edit an alignment one only needs four types of operations:

OPERATIONKEYS
set a vertical selection for ALL sequences in the alignmentDouble-Click
add white space by hitting the Space barSpaceBar

remove white spaceBackspace
select a sub-block for shiftingDrag Left-Mouse-Button
shift the selected block next to a gapped areaRight and Left Arrows

9.5.2 Save, Print and Delete


To save your alignment as a picture:

Full-width:

Asis: As displayed in GUI.

60: 60 residues width

To save an alignment or tree:

To print an alignment or tree:

To delete an alignment or tree:

9.5.3 Add a Comment


To add a comment to an alignment:

NOTE: The length of text added in a comment line can only be as long as the selected region in the alignment. However, there are up to 3 comment lines which you can add.

To display and undisplay comments:

To edit a comment:

9.5.4 Phylogenetic Trees


NOTE: Before constructing a phylogenetic tree you need to align the sequences as described in the alignment section

To view a tree:

The tree will be displayed in the editor as shown below:

To display the tree alone without the alignment:

Tree functionality:

9.5.5 Coloring an Alignment.


To color an alignment:

There are a number of ways to color an alignment in ICM. ICM offers a wide range of default coloring options to choose from in the Alignment Editor.

NOTE: You can keep selecting from the list until you find an appropriate color scheme. See the ICM language manual for other ways of coloring, definitions of color schemes and customizing the color. The colors are shaded from pale to bright where the brighter color represents higher conservation at that point in a multiple alignment.

To see the alignment color key:

To color by strength of consensus:

To color your multiple alignment by the strength of consensus at each point in an alignment:

9.5.6 Shading and Boxing an Alignment


To shade an alignment:

To box an alignment

9.5.7 Alignment View Options


The alignment view options are located on the right hand side of the alignment editor.

To add or remove the alignment title:

To rename an alignment:

To add or remove the alignment consensus display.

If you have a large alignment it may be convenient to show the number of each sequence

To number your alignment:

Horizontal Scroll

To view the alignment in Horizontal scroll click on the "Horizontal scroll" button in the View Options panel in the Alignment tool bar.

To view the sequence offset number for each of your sequences in an alignment:

To view the sequence ruler:

To view secondary structure.

If one of the sequences of the alignment is linked to a structure then you can display the secondary structure by:

The secondary structure will be displayed at the bottom of the alignment.

9.5.8 Alignment Gaps


To make an alignment clearer you may wish to HIDE gap regions.

To hide all gap regions:

The gaps in your alignment will be hidden according to the preference made in the alignment tools panel shown below. Click on the drop down arrow in the "Hidden block format" data entry box.

Two parameters can be specified directly from the Tools Panel in the alignment window:

  1. the "Hidden Block Format can use the following special symbols: e.g. " %f .. %t " or " %L "
  2. the "Hidden block width" which defines the total length of the hidden section.

Some predefined hidden block formats are shown here:

length: displays the length of the gap

length: displays the length of the gap in <>.

clean0: displays no indication of a gap

clean1: displays grey panel in the gap position.

clean2: displays a wider grey panel in the gap position

NOTE: The width of the hidden panel can be changed as shown below.

If you have hidden all the gaps individual gaps (or blocks) can be displayed by:

To show all gaps:

9.5.9 Searching an Alignment


If you have a large alignment and you wish to find a specific group of amino acids within that residue the you can use the Alignment search tool.

NOTE: Another way of searching an alignment is to use the alignment selection tools which are linked to the ICM workspace and 3D graphical window. This is described in the section entitled Making Selections in Alignments.

9.5.10 Making Alignment Selections


ICM has a very powerful alignment selection tool which enables sequences and structures to be interlinked with the 3D graphical window, the alignment window and the ICM workspace.

9.5.11 Basic Alignment Selections


To select a single column of an alignment:

To select parts of an alignment:

To select multiple discontinuous parts of an alignment:

To enable the easy selection of all sequences in an alignment:

NOTE: All selections made in the alignment window are linked to the 3D graphics window and the ICM workspace if a structure is in the alignment.

9.5.12 Select by Consensus


This is a very useful tool, for example, you may want to color the consrved regions of your structure in the 3D display windowa different color to the rest of the structure. This tool allows you to select the conserved regions in the sequence alignment. Once the selection has been made it can be used for a number of different ICM operations such as coloring and displaying secondary structure.

A selection can be made based on the alignment consensus. The buttons relating to this are in the alignment tool panel.

Before selecting by consensus you first need to define a consensus strength:

Once the selection has been made it can be used for a number of different ICM operations such as coloring and displaying secondary structure.

To invert a selection:

To hide a selection.

NOTE: All selections made in the alignment window are linked to the 3D graphics window and the ICM workspace if a structure is in the alignment.


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