
                              EMBOSS: pepinfo
     _________________________________________________________________
   
                                Program pepinfo
                                       
Function

   Plots simple amino acid properties in parallel
   
Description

   pepinfo detects and displays various useful metrics about a protein
   sequence.
   
   It can plot and display the following properties:
     * plots of hydrophobicity (using the method of Kyte & Doolittle), of
       OHM (Sweet & Eisenberg), or of consensus parameters (Eisenberg et
       al))
     * a histogram of the presence of residues with the physico-chemical
       properties: Tiny, Small, Aliphatic, Aromatic, Non-polar, Polar,
       Charged, Positive, Negative.
       
   The data are also written out to a data file.
   
Usage

   Here is a sample session with pepinfo.
   
% pepinfo
Plots simple amino acid properties in parallel
Input sequence: sw:opsd_human
Graph type [x11]:
Output file [pepinfo.out]:

   Click here to see the histogram
   
   Click here to see the hydrophobicity plots
   
Command line arguments

   Mandatory qualifiers:
  [-inseq]             sequence   Sequence USA
   -graph              xygraph    Graph type
  [-outfile]           outfile    Output file name

   Optional qualifiers:
   -hwindow            integer    Window size for hydropathy averaging
   -aaproperties       string     User defined amino acid properties
   -aahydropathy       string     User defined hydropathy data

   Advanced qualifiers:
   -[no]generalplot    bool       plot histogram of general properties
   -[no]hydropathyplot bool       plot graphs of hydropathy

   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
   [-inseq]
   (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
   [-outfile]
   (Parameter 2) Output file name Output file pepinfo.out
   Optional qualifiers Allowed values Default
   -hwindow Window size for hydropathy averaging Integer 1 or more 9
   -aaproperties User defined amino acid properties Any string is
   accepted Eaa_properties.dat
   -aahydropathy User defined hydropathy data Any string is accepted
   Eaa_hydropathy.dat
   Advanced qualifiers Allowed values Default
   -[no]generalplot plot histogram of general properties Yes/No Yes
   -[no]hydropathyplot plot graphs of hydropathy Yes/No Yes
   
Input file format

   It reads in a protein sequence.
   
Output file format

   Graphs are written to the selected graphics device.
   
   The output file contains the coordinates from the graphs.
   
   For the first set of graphs, 9 sets of true/false values are written
   out. For the second set of graphs, 3 sets of hydrophobicity values are
   written.
   
Printing out Tiny residues in OPSD_HUMAN from position 1 to 348

Position  Residue                       Result
       1       M                               0
       2       N                               0
       3       G                               1
       4       T                               1
       5       E                               0
       6       G                               1
       7       P                               0
       8       N                               0
       9       F                               0
      10       Y                               0

....................

     341       E                               0
     342       T                               1
     343       S                               1
     344       Q                               0
     345       V                               0
     346       A                               1
     347       P                               0
     348       A                               1



Printing out Small residues in OPSD_HUMAN from position 1 to 348

Position  Residue                       Result
       1       M                               0
       2       N                               1
       3       G                               1
       4       T                               1
       5       E                               0
       6       G                               1
       7       P                               1
       8       N                               1
       9       F                               0
      10       Y                               0

Data files

   The physico-chemical properties of the residues are read from the
   EMBOSS data file 'Eaa_properties.dat'. This file can be copied into
   your current directory and inspected ot altered by using the
   application 'embossdata -fetch'. Another file can be specified using
   the qualifier '-aaproperties'.
   
   The hydropathy data of the residues are read from the EMBOSS data file
   'Eaa_hydropathy.dat'. This file can be copied into your current
   directory and inspected ot altered by using the application
   'embossdata -fetch'. Another file can be specified using the qualifier
   '-aahydropathy'.
   
   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by EMBOSS
   environment variable EMBOSS_DATA.
   
   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".
   
   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata
       
Notes

   None.
   
References

    1. Kyte J, Doolittle RF A simple method for displaying the
       hydropathic character of a protein. J Mol Biol 1982 May
       5;157(1):105-132
    2. Sweet RM, Eisenberg D Correlation of sequence hydrophobicities
       measures similarity in three-dimensional protein structure. J Mol
       Biol 1983 Dec 25;171(4):479-488
    3. Eisenberg D, Weiss RM, Terwilliger TC. The helical hydrophobic
       moment: a measure of the amphiphilicity of a helix. Nature 1982
       Sep 23;299(5881):371-4
       
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with a status of 0.
   
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
   pepstats Protein statistics
   pepwindow Displays protein hydropathy
   pepwindowall Displays protein hydropathy of a set of sequences
   
Author(s)

   This application was written by Mark Faller (mfaller@hgmp.mrc.ac.uk)
   
History

   Written (1999) - Mark Faller
   
Target users

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