pepwheel

pepwheel

pepwheel displays peptide sequences in a helical representation.

Here is a sample session with pepwheel:

% pepwheel sw:hbb_human -send 30 Shows protein sequences as helices Graph type [x11]:

Mandatory qualifiers (bold if not always prompted):

[-sequence] (sequence)

Sequence USA.

-outfile (outfile)

Output filename.

-graph (graph)

Graph type.

Optional qualifiers (bold if not always prompted):

-steps (integer)

The number of residues plotted per turn is this value divided by the turns value.

-turns (integer)

The number of residues plotted per turn is the steps value divided by this value.

-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:

-[no]wheel (boolean)

Plot the wheel.

-amphipathic (boolean)

If this is true, the residues ACFGILMVWY are marked as squares, and all other residues are unmarked. This overrides any other markup you may have specified using the -squares, -diamonds, or -octags qualifiers.

-data (boolean)

Output the match data to a file instead of plotting it.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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