
                               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

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   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,
   png 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

   Any protein sequence USA.
   
Output file format

   An image is displayed.
   
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It exits with a status of 0.
   
Known bugs

   None.
   
See also

   Program name Description
   abiview Reads ABI file and display the trace
   cirdna Draws circular maps of DNA constructs
   garnier Predicts protein secondary structure
   helixturnhelix Report nucleic acid binding motifs
   hmoment Hydrophobic moment calculation
   lindna Draws linear maps of DNA constructs
   pepcoil Predicts coiled coil regions
   pepwheel Shows protein sequences as helices
   prettyplot Displays aligned sequences, with colouring and boxing
   prettyseq Output sequence with translated ranges
   remap Display a sequence with restriction cut sites, translation etc
   seealso Finds programs sharing group names
   showalign Displays a multiple sequence alignment
   showdb Displays information on the currently available databases
   showfeat Show features of a sequence
   showseq Display a sequence with features, translation etc
   textsearch Search sequence documentation text. SRS and Entrez are
   faster!
   tmap Displays membrane spanning regions
   
Author(s)

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

   Writte (2000) - Alan Bleasby
   
Target users

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