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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 information available is close to the same information given in the ‘sequence information window’ (see below), but in the frame it is updated dynamically. The individual terms are initially hidden, but can be expanded by clicking on the small ‘+’, changing it into a ‘-‘.
The GPMAW program is primarily intended as a tool for mass spectrometric analysis of proteins and peptides. However, a number of other bioinformatics tools have been included, so the use of the program extends far beyond simple mass analysis.
The coloring of residues is done through a simple edit box (right). Three colors are available (presented in the left-hand column) Setup, and for each color you can have four different entries (max. 10 residues in each entry). Notice that the question mark can substitute for ‘any residue’ (do not use ‘X’ as this is recognized as a specific residue – unknown). If the ‘Highlight global’ check-box is checked, all currently open sequence windows will be colored. If the ‘Keep highlight’ is not checked, the entries will be cleared whenever the ‘Highlight residues’ dialog is accessed.
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