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Sequence window
The sequence window is the default view of a sequence. From here you can call most of other sequence related functions (either thrugh the menu, the toolbar, or the pop-up menu).
The display can be configured in various ways, 1- or 3-letter display, average mass/monoisotopic mass, fixed residue width, sidebar with sequence information, show disulfide bridges etc. By highlighting part of the sequence you can easily obtain the mass of the given section. For easy navigation you can color specific residues (three different colors and underlining are available).
Most of the settings can easily be pre-set in the System setup box.
The sequence window is the parent window from which a large number of derived daughter windows can be created:
Peptide window
Ms/ms window
Mass search, composition search
Graphs: Hydrophobicity, secondary structure, charge vs. pH, dot-plot, alpha-helical wheel
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