pepwindowall

Function

Description

pepwindow draws a set of superimposed Kyte & Doolittle hydropathy plots for a set of protein sequences.

Algorithm

pepwindow calculates hydropathy in windows of a specified size over the input sequences.

Usage

Command line arguments

Input file format

pepwindowall reads any protein sequence USA for one or more aligned sequences.

Output file format

An image is displayed on the specified graphics device.

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

In calculating hydropathy, pepwindowall can use any of the amino acid parameters from the database of "Nakai et al." which are now included in the database AAINDEX. Before running pepwindow, you must first extract the required data files from AAINDEX (see "Data Files" section).

The result of running pepwindowall 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 an alignment.

References

  1. 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.

Author(s)

History

Target users

Comments