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You are now ready to use ClustalW from GPMAW. When working in GPMAW you open the sequences to align on the desktop, select Search | ClustalW from the menu, and you will be greeted by a dialog box where you can select and edit the names of the sequences on the desktop.
The underlines are controlled from the pop-up menu in the sequence window and the relevant daughter windows. For more information see the manual and the on-line help.
The 1/3 button toggles between 1- and 3-letter code (i.e. KTA vs Lys-Thr-Ala). When you toggle between the two modes, all selections, highlights, coloring, links etc. are conserved. The default setting is done in Setup; separately on the ‘Peptide’ AND the ‘Display’ page for the peptide and sequence windows respectively.
The status bar is initially green, but turns yellow and red as you get close to full capacity of the file. Furthermore, when a protein is selected, the basic information is displayed in the right-hand information box.
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