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.:

Basic operations

Mouse:

Menus

Toolbar

From left to right

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
Contents