pepinfo

Function

Description

pepinfo plots various amino acid properties in parallel for an input protein sequence. The types of plot available are i. Hydrophobicity plots using the method of Kyte & Doolittle, the optimal matching hydrophobicity scale (OHM) of Sweet & Eisenberg, or consensus parameters (Eisenberg et al). ii. 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 an output 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:

Notes

For calculating the hydrophobicity plots, hdrophobicity is calculated in windows of a specified size over the sequence.

The optimal matching hydrophobicity scale (OHM) scale is based on the likelihood of a given amino acid to be replaced by another hydrophobic or "buried" amino acid.

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.

Author(s)

History

Target users

Comments