EMBOSS: pepwindowall

| pepwindowall

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## Function

Draw Kyte-Doolittle hydropathy plot for a protein alignment

## Description

pepwindowall draws a set of superimposed Kyte & Doolittle hydropathy plots for a set of alignedprotein sequences.

## Algorithm

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

## Usage

Here is a sample session with pepwindowall

    % pepwindowall globins.msf -gxtitle="Base Number" -gytitle="hydropathy"
    Draw Kyte-Doolittle hydropathy plot for a protein alignment
    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

    Draw Kyte-Doolittle hydropathy plot for a protein alignment
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-sequences]         seqset     File containing a sequence alignment
      [-graph]             xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tek, tekt, none, data, xterm, png, gif, pdf,
                                      svg)

       Additional (Optional) qualifiers:
       -datafile           datafile   [Enakai.dat] AAINDEX entry data file
       -window             integer    [19] Window size (Integer from 1 to 200)
       -normalize          boolean    [N] Normalize data values

       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
       -scircular1         boolean    Sequence is circular
       -sformat1           string     Input sequence format
       -iquery1            string     Input query fields or ID list
       -ioffset1           integer    Input start position offset
       -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
       -gdesc2             string     Graph description
       -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 first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to 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 and exit. 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 dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequences] (Parameter 1) | seqset | File containing a sequence alignment | Readable set of sequences | Required
[-graph] (Parameter 2) | xygraph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg | EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers
-datafile | datafile | AAINDEX entry data file | Data file | Enakai.dat
-window | integer | Window size | Integer from 1 to 200 | 19
-normalize | boolean | Normalize data values | Boolean value Yes/No | No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequences" associated seqset qualifiers
-sbegin1 -sbegin_sequences | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequences | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequences | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequences | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequences | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequences | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequences | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequences | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequences | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_sequences | string | Input sequence format | Any string |
-iquery1 -iquery_sequences | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequences | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequences | string | Database name | Any string |
-sid1 -sid_sequences | string | Entryname | Any string |
-ufo1 -ufo_sequences | string | UFO features | Any string |
-fformat1 -fformat_sequences | string | Features format | Any string |
-fopenfile1 -fopenfile_sequences | string | Features file name | Any string |
"-graph" associated xygraph qualifiers
-gprompt2 -gprompt_graph | boolean | Graph prompting | Boolean value Yes/No | N
-gdesc2 -gdesc_graph | string | Graph description | Any string |
-gtitle2 -gtitle_graph | string | Graph title | Any string | Kyte-Doolittle Plot
-gsubtitle2 -gsubtitle_graph | string | Graph subtitle | Any string |
-gxtitle2 -gxtitle_graph | string | Graph x axis title | Any string | Sequence
-gytitle2 -gytitle_graph | string | Graph y axis title | Any string | Hydropathy
-goutfile2 -goutfile_graph | string | Output file for non interactive displays | Any string |
-gdirectory2 -gdirectory_graph | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

pepwindowall reads aligned protein sequence.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier `-sformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

### 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: 0.61
      Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.65
      Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.65
      Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.83
      Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 1.00
      Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.91
      Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.43

    //

               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

The output is to the specified graphics device.

The results can be output in one of several formats by using the command-line qualifier -graph xxx, where 'xxx' is replaced by the name of the required device. Support depends on the availability of third-party software packages.

The device names that output to a file are: ps (postscript), cps (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.

The other available device names are: meta, x11 (xwindows), tek (tek4107t), tekt (tektronix), xterm, text.

Output can be turned off by specifying none (null).

See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further information on supported devices.

### Output files for usage example

### Graphics File: pepwindowall.ps

## Data files

pepwindowall 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

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 pepwindowall, 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.

## See also

Program name | Description
--- | ---
charge | Draw a protein charge plot
hmoment | Calculate and plot hydrophobic moment for protein sequence(s)
iep | Calculate the isoelectric point of proteins
octanol | Draw a White-Wimley protein hydropathy plot
pepinfo | Plot amino acid properties of a protein sequence in parallel
pepstats | Calculate statistics of protein properties
pepwindow | Draw a hydropathy plot for a protein sequence

## Author(s)

Ian Longden formerly at:
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## 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