Pepwindow

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PEPWINDOW(+)

FUNCTION

PepWindow plots measures of protein hydrophobicity according to the method of Kyte and Doolittle.

DESCRIPTION

PepWindow plots measures of protein hydrophathy according to the method of Kyte & Doolittle (J.Mol. Biol.(1982) 157:105-132). The curve, by default, is an average of a residue specific hydrophathy index over a window of nine residues (the default value). When the line is in the upper part of the frame, it indicates a hydrophobic region, and when the line is in the lower half, a hydrophilic region. An alternative curve, depicting the median value passed through a cascade of median filters (Bangham, J.A. , Anal. Biochem. 174, 142-145 (1988)) can be obtained by adding -MESH= x on the command line.

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 PepWindow 

  
  
  % pepwindow
  
   PEPWINDOW uses protein sequence data
  
   PEPWINDOW of what sequence ?  Sw:Achg_Torca
  
              Start (* 1 *) ?
              End (* 506 *) ?
  
   The minimum density for a one-page plot is 440.0 residues/100 platen
   units. What density do you want (* 440.0 *) ?
  
  %

OUTPUT

These are the plots from the example session

RESTRICTIONS

None known.

CONSIDERATIONS

PepWindow output displays the distribution of polar and apolar residues along a sequence. The plot may be used to spot putative membrane-buried segments and exposed parts such as antigenic determinants, or to compare distantly related sequences to see if some charactersitic pattern of hydrophobicity has been preserved. PepWindow plots default to a running average curve. The qualifier MESH=x will plot a median sieved through a cascade of median filters. Care should be taken when using this plot as it increases the contrast of the data but provides no image enhancement.

SUGGESTIONS

Window values of 5-7 residues seem appropriate for finding surface- exposed regions that might be antigenic sites, whereas windows of 19-21 residues will make long, hydrophobic membrane spanning segments stand out more clearly. PepWindow uses a default window of 9. This value can be changed by using the qualifier -WINdow= 19. Mesh values from 2 to 25 are allowed. Increasing -MESH= x values over which the median is calculated results in a reduction of of ther signal to a line with little contrast. Recommended values are -MESH= 11 which should show membrane spanning regions capable of crossing the membrane twice.

INPUT FILE

The input file for PepWindow is a protein sequence file.

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.

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: % pepwindow [-INfile=]Sw:Achg_Torca -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=506        the range of interest
  -DENsity=87              density in residues/100 platen units
  
  Local Data Files: None
  
  Optional Parameters:
  
  -TITLEText               user defined title text
  -YLABELText              user defined y-axis label
  -XLABELText              user defined x-axis label
  -YMAX=5.0                maximum value on y-axis
  -INDEXline=1.3           displays index line at y-axis pos. 1.3
  -MARK=achg_torca.mrk     marks x-axis
  -SHOWSeq                 displays the sequence
  -NOPLOt                  suppresses the whole plot
  -WINdow=9                sets the window for hydropathy averaging
  -LABHeight=1.5           axis label and title character height
  -BOXES                   makes a box around each quantitative panel
  -MESH=2                  calculates median rather than mean
  
  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

LOCAL DATA FILES

The files described below supply auxiliary data to this program. The program automatically reads them from a public data directory unless you either 1) have a data file with exactly the same name in your current working directory; or 2) name a file on the command line with an expression like -DATa1=myfile.dat. For more information see Chapter 4, Using Data Files in the User's Guide.

If you are studying a sequence with known features, this program marks the plot with small boxes showing the positions of these features. The presence of a file in your directory with the same name as your sequence and the file name extension .mrk causes the program to mark each range specified in the file. You can provide a marking file on the command line with an expression like -MARk= achg_torca.mrk. The file gamma.mrk contains information about the format of marking files. The figure for the example session shows marked regions.

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.

-OUTfile=achg_torca.win

writes the calculated values to a file.

-TITLEText="Plot title"

sets the title for the top of the plot, overriding the default.

-YLABELText="Hydrophobicity"

sets the text for the y-axis (hydrophobicity), overriding the default.

-XLABELText="Residue position"

sets the text for the x-axis (sequence), overriding the default.

-YMAX=5.0

sets the maximum values for the y-axis to +/-YMAX.

-INDEXline=1.3

draws an additional horizontal line to mark regions of high hydrophobicity.

-SHOWSeq

shows the sequence at the top of the plot.

-NOPLOt

suppresses the entire plot

-WINdow=9

sets the window size. A value of 9 is reasonable for general use, but a higher value (for example 19) is preferable for the identification of potential membrane-spanning regions.

-LABHeight=1.5

sets the character height for the axis labels and title.

-BOXES

Makes a box around each panel.

-MESH=2

calculates the median (middle value in an ordered list) rather than the mean over the window.

-MARk=achg_torca.mrk

If you are studying a sequence with known features, this program marks the plot with small boxes showing the positions of these features. The presence of a file in your directory with the same name as your sequence and the file name extension .mrk causes the program to mark each range specified in the file. The file gamma.mrk contains information about the format of marking files.

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.

REFERENCES

Kyte, J. and Doolittle, R.F. (1982) "A Simple Method for Displaying the Hydropathic Character of a Protein." Journal of Molecular Biology 157, 105-132.

Bangham, J.A. (1988) "Data-sieving hydrophobicity plots." Anal. Biochem. 174, 142-45.

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