| 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 globins.msf -gxtitle="Base Number" -gytitle="hydropathy"
    Displays protein hydropathy of a set of sequences
    Graph type [x11]: cps

    Created pepwindowall.ps

Go to the input files for this example
Go to the output files for this example

## Command line arguments

Standard (Mandatory) qualifiers: [-sequences] seqset File containing a sequence alignment [-graph] xygraph Graph type Additional (Optional) qualifiers: -datafile datafile Aaindex database file -length integer Window size Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequences" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-graph" associated qualifiers -gprompt2 boolean Graph prompting -gtitle2 string Graph title -gsubtitle2 string Graph subtitle -gxtitle2 string Graph x axis title -gytitle2 string Graph y axis title -goutfile2 string Output file for non interactive displays -gdirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequences] (Parameter 1) | File containing a sequence alignment | Readable set of 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, xml | EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers | Allowed values | Default
-datafile | Aaindex database file | Data file | Enakai.dat
-length | Window size | Integer from 1 to 200 | 7
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

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

### Input files for usage example

### File: globins.msf

    !!AA_MULTIPLE_ALIGNMENT 1.0

      ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..

      Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.14
      Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.15
      Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.15
      Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.19
      Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 0.23
      Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.21
      Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.10

    //

               1                                               50
    HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
    HBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
    HBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
    HBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
    MYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
    GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
    LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD

               51                                             100
    HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
    HBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
    HBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
    HBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
    MYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
    GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
    LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN

               101                                            150
    HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
    HBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
    HBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
    HBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
    MYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
    GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
    LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA

               151        164
    HBB_HUMAN  NALAHKYH~~~~~~
    HBB_HORSE  NALAHKYH~~~~~~
    HBA_HUMAN  TVLTSKYR~~~~~~
    HBA_HORSE  TVLTSKYR~~~~~~
    MYG_PHYCA  KDIAAKYKELGYQG
    GLB5_PETMA Y~~~~~~~~~~~~~
    LGB2_LUPLU IVIKKEMNDAA~~~

## Output file format

An image is displayed on the specified graphics device.

### Output files for usage example

### Graphics File: pepwindowall.ps

## Data files

pepwindow reads the Kyte-Doolittle hydropathy data from the file 'Enakai.dat'

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

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

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

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.

## 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
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
mwcontam | Shows molwts that match across a set of files
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)

Ian Longden (il © sanger.ac.uk)
Sanger Institute, 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

None