Pepnet

• PEPNET(+)
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • RELATED PROGRAMS
  • RESTRICTIONS
  • CONSIDERATIONS
  • SUGGESTIONS
  • INPUT FILE
  • COMMAND-LINE SUMMARY
  • GRAPHICS
  • CTRL-C
  • OPTIONAL PARAMETERS
    • -CIRcles
    • -NOCIRcles
    • -DIAmonds
    • -NODIAmonds
    • -SQUares
    • -NOSQUares
    • -FIGure
    • -FONT
    • -COLor
    • -SCAle
    • -XPAN
    • -YPAN
    • -PORtrait

PEPNET(+)

FUNCTION

PepNet is a program to view the two-dimensional helical representation of protein sequences.

DESCRIPTION

HelicalNet is an alternative to the 'statistical' approach offered by other GCG secondary prediction programs such as PepPlot. The periodic distribution of amino acids on an ideal alpha-helix can be best appreciated where one is looking at a cylindrical projection that has been slit open and folded out flat. The 3.6-residue pitch of the helix brings residues i, i+/-3, and i,+/-4 together; similarly, in a beta-sheet, residues i and i+/-2 are neighbours on the same side of the sheet.

AUTHOR

This program was written by Rodrigo Lopez S. (E-mail: rodrigol@biotek.uio.no; Post: Biotechnology Centre of Oslo, PO Box 1125 Blindern, N-0317 Oslo 3, Norway).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).

EXAMPLE

Here is a session with PepNet

  
  
  % pepnet
  
   PEPNET uses protein sequence data
  
   PEPNET of what sequence ?  Sw:fos_human
  
              Start (* 1 *) ?
              End  (* 380 *) ? 211
  
  %
  

OUTPUT

This is the plot from the example session

In the example, residues 165 to 193 form a leucine zipper motif.

RELATED PROGRAMS

PepWheel is a program to view the periodic distribution of amino acid residues in protein sequences. PepCoil identifies potential coiled-coil regions of protein sequences using the algorithm of Lupas A, van Dyke M & Stock J (1991). HelicalWheel plots a peptide sequence as a helical wheel to help you recognize amphiphilic regions.

RESTRICTIONS

None known.

CONSIDERATIONS

PepNet s output generates the 2-D-helical representation necessary for hydrophobic cluster analysis. As with other secondary structure prediction schemes care should be taken interpreting the results.

SUGGESTIONS

Once the user identifies a segment of interest on a sequence, (s)he can then plot the required sequence stretch with another run of PepNet to obtain the best view of residue clustering.

INPUT FILE

The input file for PepNet is a protein sequence file.

COMMAND-LINE SUMMARY

All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  
  
  Minimum Syntax: % pepnet [-INfile=]Sw:Fos_Human -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=221       the range of interest
  
  Local Data Files: None
  
  Optional Parameters:
  
  -CIRcles=HKR            circles on all basic residues
  -NOCIRcles              no residues marked as cicrles
  -DIAmonds=DENSQT        diamonds on all acidic residues
  -NODIAmonds             no residues marked as diamonds
  -SQUares=ILVM           squares on all small hydrophobic residues
  -NOSQUares              no residues marked as squares
  
  Most EGCG graphics programs accept these and other switches. See the Using
  Graphics chapter of the EGCG USERS GUIDE for descriptions.
  
  -DENSity=150.0        plot density in bases per 100 platen units
  -LEFTMARgin=10.0      sets the left plot margin position
  -RIGHTMARgin=140.0    sets the right plot margin position
  -BOTTOMMARgin=10.0    sets the bottom plot margin position
  -TOPMARgin=90.0       sets the top plot margin position
  -BORDer               puts a line border around the plot
  -NOBORDer             suppresses a line border
  -PAGENUMber           forces page numbering
  -NOPAGENUMber         suppresses page numbering
  -TITletext="text"     overrides the default plot title
  -NOTITletext          suppresses the plot title
  -SUBTITletext="text"  overrides the default plot subtitle
  -NOSUBTITletext       suppresses the plot subtitle
  -CHEIGHT=1.5          default plot character height
  -LINESTyle1=1         plot line style 1 (set for each line)
  -LINEPERiod1=1        plot line period 1 (set for each line)
  -LINECOLor1=0         plot line colour 1 (set for each line)
  All GCG graphics programs accept these and other switches. See the Using
  Graphics chapter of the USERS GUIDE for descriptions.
  
  -FIGure[=FileName]  stores plot in a file for later input to FIGURE
  -FONT=3             draws all text on the plot using font 3
  -COLor=1            draws entire plot with pen in stall 1
  -SCAle=1.2          enlarges the plot by 20 percent (zoom in)
  -XPAN=10.0          moves plot to the right 10 platen units (pan right)
  -YPAN=10.0          moves plot up 10 platen units (pan up)
  -PORtrait           rotates plot 90 degrees
  

GRAPHICS

The Wisconsin Package must be configured for graphics before you run any program with graphics output! If the % setplot command is available in your installation, this is the easiest way to establish your graphics configuration, but you can also use commands like % postscript that correspond to the graphics languages the Wisconsin Package supports. See Chapter 5, Using Graphics in the User's Guide for more information about configuring your process for graphics.

CTRL-C

If you need to stop this program, use C to reset your terminal and session as gracefully as possible. Searches and comparisons write out the results from the part of the search that is complete when you use C. The graphics device should stop plotting the current page and start plotting the next page. If the current page is the last page, plotters should put the pen away and graphic terminals should return to interactive mode.

OPTIONAL PARAMETERS

The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

-CIRcles=HKR

draw circles around all basic residues.

-NOCIRcles

cancels the default drawing of circles around all basic residues.

-DIAmonds=DENSQT

draw diamonds around all acidic residues.

-NODIAmonds

cancels the default drawing of diamonds around all acidic residues.

-SQUares=ILVM

draw squares around all small hydrophobic residues.

-NOSQUares

cancels the default drawing of squares around all hydrophobic residues.

These options apply to all GCG graphics programs. These and many others are described in detail in Chapter 5, Using Graphics of the User's Guide.

-FIGure=programname.figure

writes the plot as a text file of plotting instructions suitable for input to the Figure program instead of drawing the plot on your plotter.

-FONT=3

draws all text characters on the plot using Font 3 (see Appendix I) .

-COLor=1

draws the entire plot with the pen in stall 1.

These options let you expand or reduce the plot (zoom), move it in either direction (pan), or rotate it 90 degrees (rotate).

-SCAle=1.2

expands the plot by 20 percent by resetting the scaling factor (normally 1.0) to 1.2 (zoom in). You can expand the axes independently with -XSCAle and -YSCAle. Numbers less than 1.0 contract the plot (zoom out).

-XPAN=30.0

moves the plot to the right by 30 platen units (pan right).

-YPAN=30.0

moves the plot up by 30 platen units (pan up).

-PORtrait

rotates the plot 90 degrees. Usually, plots are displayed with the horizontal axis longer than the vertical (landscape). Note that plots are reduced or enlarged, depending on the platen size, to fill the page.

Printed: April 22, 1996 15:54 (1162)