Overview |
This chapter gives an overview of Alignment Editor components and explains basic concepts of browsing the alignment. It includes the following sections:
Alignment Editor is a powerful tool for visualization and editing DNA, RNA or protein multiple sequence alignments. The editor supports different MSA formats, such as ClustalW, MSF, Stockholm. Full list of file formats supported in UGENE is here.
The editor provides interactive visual representation which includes:
Using Alignment Editor you can:
In this section we will get acquainted with Alignment Editor components.
Here is the default layout of editor:
This is the main component of the editor. It displays aligned sequences. The upper part of the Sequence Area is the ruler, which shows the coordinates of currently visible row sequences.
This component is situated above the Sequence Area. It shows the consensus sequence for current alignment calculated using currently selected algorithm.
This component is situated to the right of the Sequence Area. It shows names of corresponding sequences in the alignment.
The toolbar contains shortcuts for important editor actions, such as Undo/Redo, Zooming and others.
These are the offsets for first and last visible base for each alignment row. Note that the offset value doesn't include gaps.
For example, let's assume that the coordinate of first visible base of the row is N, but the row contains K gaps before the position N. The starting offset value will be N - M. The same rule is true for ending offset.
You can turn off Sequence offsets using Main menu->Actions->View or Context menu->View by unchecking Show offsets action.
This component displays the coordinates of upper left corner of current selection. If no region is selected it shows the starting alignment point.
As in the Sequence view this component shows whether the alignment is locked. Locked documents are not allowed to be modified.
Sequence area provides several flexible ways to navigate through the alignment.
The most simple way is to use mouse and scrollbars.
Alternatively you can use arrow keys on the keyboard to navigate.
List of hot keys for quick navigation:
| PgUp | Move one screen left |
| PgDown | Move one sreen right |
| Home | Center the starting columns of the alignment |
| End | Move to the trailing columns of the alignment |
Finally you can use "Go to positon" dialog from Actions menu, context menu or editor toolbar.
Enter the column number (base coordnate) and the view will be centered to the corresponding base.
There are various coloring schemas for DNA and amino alphabets available.
To change the schema, activate context menu (right mouse button) or Actions menu from main toolbar and execute select the required schema from Colors submenu.
To perform zoom operations use corresponding buttons on the editor toolbar.
You can zoom to the selected region by clicking "Zoom to selection" button. It is very convenient operation, when the alignment size is rather large. For example, you can zoom out to some percentage, select interesting region and then zoom to the selection.
You can change font by clicking "Change font" button.
To reset zoom and font click "Reset zoom" button.
You can search for pattern inside the alignment.
Enter the query string in the edit box under the Sequence area.
If the pattern is found, the result will be focused and highlighted in the Sequence area. You can continue the search in any direction from this position.
The are several modes included:
Based on JalView algorithm. Returns '+' if there are 2 characters with high frequency. Returns symbol in lower case if the symbol content in a row is lower than the specified threshold.
Emulates ClustalW program and file format behavior.
This algorithm is proposed by Victor Levitsky to calculate consensus of DNA alignments. At first, it collects global alignment frequencies for every symbol using extended (15 symbols) DNA alphabet. Then, for every column it selects the most rare symbol in the whole alignment with percentage in the column greater or equals to the threshold value.
The algorithm returns gap character ('-') if symbol frequency in a column is lower than threshold specified.
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