DNAMAN provides graphic presentations of hydrophobic and hydrophilic profiles of the current protein sequence. The plot is based on the method developed by Hopp and Woods (1981). The hydrophobic properties of a protein may help you to locate hydrophobic clusters and hydrophilic properties can be used to find potential antigen positions in the protein sequence. For more information about plotting methodology, please refer to Hopp and Woods (1981) and Kyte and Doolittle (1982).
Choose the Protein | Hydrophobic Profile | Current Sequence or Protein | Hydrophobic Profile | Current Sequence command to display the profile of the current protein sequence in a graphic window. You may also choose the All Available Sequences menu if you like to compare the profiles of all available protein sequences in channels.
The plot shows the hydrophobicity or hydrophilicity of an amino acid against its position. Averaging the values of a group of neighbor amino acids can smooth the profile. The average group length is defined by Window Size in the Options dialog box. The default value is 6. If the Window Size is 1, the profile represents the hydrophobicity (or hydrophilicity) value of each amino acid of the protein sequence. With a value greater than 1, DNAMAN will repetitively average the hydrophobicity (or hydrophilicity) values along the peptide chain in the plot.
DNAMAN allows you to set the Y axis scale in the Options dialog box.
See the Chapter V for more information on how to handle Profile Plot.
* A Stop is indicated as a Circle.
* An unknown amino acid is indicated as a Square.