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PEPNET(1e) EMBOSS Manual for Debian PEPNET(1e)


pepnet - Draw a helical net for a protein sequence


pepnet -sequence sequence -amphipathic toggle -squares  string -diamonds string -octags string -graph graph

pepnet -help


pepnet is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Display,Protein:2D Structure" command group(s).


Input section

-sequence sequence

Output section

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

-squares string

By default the aliphatic residues ILVM are marked with squares. Default value: ILVM

-diamonds string

By default the residues DENQST are marked with diamonds. Default value: DENQST

-octags string

By default the positively charged residues HKR are marked with octagons. Default value: HKR

-graph graph


Bugs can be reported to the Debian Bug Tracking system (, or directly to the EMBOSS developers (


pepnet is fully documented via the tfm(1) system.


Debian Med Packaging Team <>
Wrote the script used to autogenerate this manual page.


This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.

05/11/2012 EMBOSS 6.4.0