EMBOSS: pepnet


Program pepnet

Function

Displays proteins as a helical net

Description

This 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.

It is therefore easy to see patterns of amphipathicity that you may wish to investigate in more detail by using displays such as pepwheel.

You can specify which residues to mark up in squares, diamonds and octagons.

Usage

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]: 

CLick here for the graph

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequence]          sequence   Sequence USA
*  -graph              graph      Graph type

   Optional qualifiers (* 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        bool       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'.
   -data               bool       Output the data to a file instead of
                                  plotting it


Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence USA Readable sequence Required
-graph Graph type EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm EMBOSS_GRAPHICS value, or x11
Optional qualifiers Allowed values Default
-squares By default the aliphatic residues ILVM are marked with squares. Any string is accepted ILVM
-diamonds By default the residues DENQST are marked with diamonds. Any string is accepted DENQST
-octags By default the positively charged residues HKR are marked with octagons. Any string is accepted HKR
Advanced qualifiers Allowed values Default
-amphipathic 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'. Yes/No No
-data Output the data to a file instead of plotting it Yes/No No

Input file format

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Program nameDescription
checktransReports STOP codons and ORF statistics of a protein sequence
digestProtein proteolytic enzyme or reagent cleavage digest
garnierPredicts protein secondary structure
helixturnhelixReport nucleic acid binding motifs
iepCalculates the isoelectric point of a protein
octanolDisplays protein hydropathy
pepcoilPredicts coiled coil regions
pepinfoPlots simple amino acid properties in parallel
pepstatsProtein statistics
pepwheelShows protein sequences as helices
pepwindowDisplays protein hydropathy
pepwindowallDisplays protein hydropathy of a set of sequences
sigcleaveReports protein signal cleavage sites

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

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