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        boolean    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               boolean    Output the data to a file instead of
                                  plotting it

   General qualifiers:
  -help                boolean    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 nameDescription
abiviewReads ABI file and display the trace
cirdnaDraws circular maps of DNA constructs
garnierPredicts protein secondary structure
helixturnhelixReport nucleic acid binding motifs
hmomentHydrophobic moment calculation
lindnaDraws linear maps of DNA constructs
pepcoilPredicts coiled coil regions
pepwheelShows protein sequences as helices
prettyplotDisplays aligned sequences, with colouring and boxing
prettyseqOutput sequence with translated ranges
remapDisplay a sequence with restriction cut sites, translation etc
seealsoFinds programs sharing group names
showalignDisplays a multiple sequence alignment
showdbDisplays information on the currently available databases
showfeatShow features of a sequence
showseqDisplay a sequence with features, translation etc
textsearchSearch sequence documentation text. SRS and Entrez are faster!
tmapDisplays 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.

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