The display can be configured in multiple ways:
1- or 3-letter display,
average mass/monoisotopic mass,
fixed residue width,
sidebar with sequence information,
display disulfide bridges, modified residues etc.
By highlighting part of the sequence you can easily obtain the mass of the given peptide(s). 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 forms the parent window from which a large number of derived daughter windows can be created:
Mass search, composition search
Graphs: Hydrophobicity, secondary structure, charge vs. pH, dot-plot, alpha-helical wheel