
                            EMBOSS: pepwindowall
     _________________________________________________________________
   
                             Program pepwindowall
                                       
Function

   Displays protein hydropathy of a set of sequences
   
Description

   pepwindowall produces a set of superimposed Kyte & Doolittle
   hydropathy plots from an aligned set of protein sequences.
   
   The result is the same as running pepwindow on a set of proteins with
   aligning gaps and superimposing the plots.
   
   It is useful for visualising the average hydropathy and its
   variability along the alignment.
   
Usage

   Here is a sample session with pepwindowall.
   
% pepwindowall globin.msf -gxtitle="Base Number" -gytitle="hydropathy"
Displays protein hydropathy of a set of sequences
Graph type [x11]:

   click here for result
   
Command line arguments

   Mandatory qualifiers:
  [-msf]               seqset     File containing a sequence alignment
  [-graph]             xygraph    Graph type

   Optional qualifiers:
   -datafile           datafile   nakai database file
   -length             integer    window size

   Advanced qualifiers: (none)
   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
   [-msf]
   (Parameter 1) File containing a sequence alignment Readable sequences
   Required
   [-graph]
   (Parameter 2) 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
   -datafile nakai database file Data file Enakai.dat
   -length window size Integer from 1 to 200 7
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   Any protein sequence USA for one or more aligned sequences.
   
Output file format

   An image is displayed.
   .ps file if postscript output requested.
   
Data files

   pepwindow reads the Kyte-Doolittle hydropathy data from the file
   'Enakai.dat'
   
   The EMBOSS data file 'Enakai.dat' contains :-
   
D Hydropathy index (Kyte-Doolittle, 1982)
R 0807099
A Kyte, J. and Doolittle, R.F.
T A simple method for displaying the hydropathic character of a protein
J J. Mol. Biol. 157, 105-132 (1982)
C CHOC760103    0.964  JANJ780102    0.922  DESM900102    0.898
  EISD860103    0.897  CHOC760104    0.889  WOLR810101    0.885
  RADA880101    0.884  MANP780101    0.881  EISD840101    0.878
  PONP800103    0.870  NAKH920108    0.868  JANJ790101    0.867
  JANJ790102    0.866  PONP800102    0.861  MEIH800103    0.856
  PONP800101    0.851  PONP800108    0.850  WARP780101    0.845
  RADA880108    0.842  ROSG850102    0.841  DESM900101    0.837
  BIOV880101    0.829  RADA880107    0.828  LIFS790102    0.824
  KANM800104    0.824  CIDH920104    0.824  MIYS850101    0.821
  RADA880104    0.819  NAKH900111    0.817  NISK800101    0.812
  FAUJ830101    0.811  ARGP820103    0.806  NAKH920105    0.803
  ARGP820102    0.803  KRIW790101   -0.805  CHOC760102   -0.838
  GUYH850101   -0.843  RACS770102   -0.844  JANJ780103   -0.845
  ROSM880101   -0.845  PRAM900101   -0.850  JANJ780101   -0.852
  GRAR740102   -0.859  MEIH800102   -0.871  ROSM880102   -0.878
  OOBM770101   -0.899
I   A/L    R/K    N/M    D/F    C/P    Q/S    E/T    G/W    H/Y    I/V
    1.8   -4.5   -3.5   -3.5    2.5   -3.5   -3.5   -0.4   -3.2    4.5
    3.8   -3.9    1.9    2.8   -1.6   -0.8   -0.7   -0.9   -1.3    4.2
//

Notes

   None.
   
References

Kyte, J. and Doolittle, R.F.
A simple method for displaying the hydropathic character of a protein
J. Mol. Biol. 157, 105-132 (1982)

Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   0 upon successful completion.
   
Known bugs

   None.
   
See also

   Program name Description
   backtranseq Back translate a protein sequence
   charge Protein charge plot
   checktrans Reports STOP codons and ORF statistics of a protein
   sequence
   compseq Counts the composition of dimer/trimer/etc words in a sequence
   emowse Protein identification by mass spectrometry
   freak Residue/base frequency table or plot
   iep Calculates the isoelectric point of a protein
   mwfilter Filter noisy molwts from mass spec output
   octanol Displays protein hydropathy
   pepinfo Plots simple amino acid properties in parallel
   pepstats Protein statistics
   pepwindow Displays protein hydropathy
   
Author(s)

   This application was written by Ian Longden (il@sanger.ac.uk)
   Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus,
   Hinxton, Cambridge, CB10 1SA, UK.
   
History

Completed 4th June 1999.

Target users

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