| ## EMBOSS: pepwindowall

# Program pepwindowall

## Function

Displays protein hydropathy of a set of sequences

## Description

pepwindowall produces a set of superimposed Kyte & Doolittle hydropathy plots from an aligned set of protein sequences.

The result 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 the alignment.

## Usage

Here is a sample session with pepwindowall.

    % pepwindowall globin.msf -gxtitle="Base Number" -gytitle="hydropathy"
    Displays protein hydropathy of a set of sequences
    Graph type [x11]:

click here for result

## Command line arguments

       Mandatory qualifiers:
      [-msf]               seqset     File containing a sequence alignment
      [-graph]             xygraph    Graph type

       Optional qualifiers:
       -datafile           datafile   nakai database file
       -length             integer    window size

       Advanced qualifiers: (none)
       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
--- | --- | ---
[-msf] (Parameter 1) | File containing a sequence alignment | Readable sequences | Required
[-graph] (Parameter 2) | 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
Optional qualifiers | Allowed values | Default
-datafile | nakai database file | Data file | Enakai.dat
-length | window size | Integer from 1 to 200 | 7
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Any protein sequence USA for one or more aligned sequences.

## Output file format

An image is displayed.
.ps file if postscript output requested.

## 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

None.

## References

    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.

## 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
pepinfo | Plots simple amino acid properties in parallel
pepstats | Protein statistics
pepwindow | Displays protein hydropathy

## Author(s)

This application was written by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

    Completed 4th June 1999.

## Target users

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

## Comments