EMBOSS: pepinfo

Program pepinfo

Function

Description

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

% 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

Output file format

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 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

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

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

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