pepnet is a method of displaying the residues of a protein in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix.

Here is a sample session with pepnet:

% pepnet -sask
Input sequence: sw:gcn4_yeast
     Begin at position [start]: 253
       End at position [end]: 274
Graph type [x11]:

Mandatory qualifiers (bold if not always prompted):

[-sequence] (sequence)

Sequence USA.

-graph (graph)

Graph type.

Optional qualifiers (bold if not always prompted):

-squares (string)

By default, the aliphatic residues ILVM are marked with squares.

-diamonds (string)

By default, the residues DENQST are marked with diamonds.

-octags (string)

By default, the positively charged residues HKR are marked with octagons.

Advanced qualifiers:

-amphipathic (boolean)

If true, the residues ACFGILMVWY are marked as squares. All other residues are not marked. This overrides any other markup you may have specified using the -squares, -diamonds, or -octags qualifiers.

-data (boolean)

Output data to a file instead of plotting it.