pepinfo
Function
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
Command line arguments
Input file format
pepinfo reads a protein sequence USA.
Output file format
Graphs are written to the selected graphics device.
The output file 'pepinfo.out' 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.
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
-
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
-
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
-
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.
Author(s)
History
Target users
Comments