EMBOSS: pepwindow

| pepwindow

## Function

--> Draw a Kyte-Doolittle hydropathy plot for a protein sequence

## Description

pepwindow draws a classic Kyte & Doolittle hydropathy plot for a protein sequence.

## Algorithm

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

## Usage

Here is a sample session with pepwindow

    % pepwindow tsw:hba_human
    Draw a Kyte-Doolittle hydropathy plot for a protein sequence
    Graph type [x11]: cps

    Created pepwindow.ps

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

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          sequence   Protein sequence filename and optional
                                      format, or reference (input USA)
       -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tekt, tek, none, data, xterm, png, gif)

       Additional (Optional) qualifiers:
       -datafile           datafile   [Enakai.dat] AAINDEX entry data file
       -length             integer    [7] Window size (Integer from 1 to 200)

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of the sequence to be used
       -send1              integer    End of the 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
       -gprompt            boolean    Graph prompting
       -gdesc              string     Graph description
       -gtitle             string     Graph title
       -gsubtitle          string     Graph subtitle
       -gxtitle            string     Graph x axis title
       -gytitle            string     Graph y axis title
       -goutfile           string     Output file for non interactive displays
       -gdirectory         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. 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Protein sequence filename and optional format, or reference (input USA) | Readable sequence | Required
-graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers | Allowed values | Default
-datafile | AAINDEX entry data file | Data file | Enakai.dat
-length | Window size | Integer from 1 to 200 | 7
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

pepwindow reads any protein sequence USA.

### Input files for usage example

'tsw:hba_human' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:hba_human

    ID   HBA_HUMAN               Reviewed;         142 AA.
    AC   P69905; P01922; Q96KF1; Q9NYR7;
    DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
    DT   23-JAN-2007, sequence version 2.
    DT   03-APR-2007, entry version 41.
    DE   Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin).
    GN   Name=HBA1;
    GN   and
    GN   Name=HBA2;
    OS   Homo sapiens (Human).
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
    OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
    OC   Catarrhini; Hominidae; Homo.
    OX   NCBI_TaxID=9606;
    RN   [1]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HBA1).
    RX   MEDLINE=81088339; PubMed=7448866; DOI=10.1016/0092-8674(80)90347-5;
    RA   Michelson A.M., Orkin S.H.;
    RT   "The 3' untranslated regions of the duplicated human alpha-globin
    RT   genes are unexpectedly divergent.";
    RL   Cell 22:371-377(1980).
    RN   [2]
    RP   NUCLEOTIDE SEQUENCE [MRNA] (HBA2).
    RX   MEDLINE=80137531; PubMed=6244294;
    RA   Wilson J.T., Wilson L.B., Reddy V.B., Cavallesco C., Ghosh P.K.,
    RA   Deriel J.K., Forget B.G., Weissman S.M.;
    RT   "Nucleotide sequence of the coding portion of human alpha globin
    RT   messenger RNA.";
    RL   J. Biol. Chem. 255:2807-2815(1980).
    RN   [3]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HBA2).
    RX   MEDLINE=81175088; PubMed=6452630;
    RA   Liebhaber S.A., Goossens M.J., Kan Y.W.;
    RT   "Cloning and complete nucleotide sequence of human 5'-alpha-globin
    RT   gene.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 77:7054-7058(1980).
    RN   [4]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RX   PubMed=6946451;
    RA   Orkin S.H., Goff S.C., Hechtman R.L.;
    RT   "Mutation in an intervening sequence splice junction in man.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 78:5041-5045(1981).
    RN   [5]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT LYS-32.
    RX   MEDLINE=21303311; PubMed=11410421;
    RA   Zhao Y., Xu X.;
    RT   "Alpha2(CD31 AGG-->AAG, Arg-->Lys) causing non-deletional alpha-
    RT   thalassemia in a Chinese family with HbH disease.";
    RL   Haematologica 86:541-542(2001).
    RN   [6]

      [Part of this file has been deleted for brevity]

    FT                                /FTId=VAR_002840.
    FT   VARIANT     131    131       A -> D (in Yuda; O(2) affinity down).
    FT                                /FTId=VAR_002842.
    FT   VARIANT     131    131       A -> P (in Sun Prairie; unstable).
    FT                                /FTId=VAR_002841.
    FT   VARIANT     132    132       S -> P (in Questembert; highly unstable;
    FT                                causes alpha-thalassemia).
    FT                                /FTId=VAR_002843.
    FT   VARIANT     134    134       S -> R (in Val de Marne; O(2) affinity
    FT                                up).
    FT                                /FTId=VAR_002844.
    FT   VARIANT     136    136       V -> E (in Pavie).
    FT                                /FTId=VAR_002845.
    FT   VARIANT     137    137       L -> M (in Chicago).
    FT                                /FTId=VAR_002846.
    FT   VARIANT     137    137       L -> P (in Bibba; unstable; causes alpha-
    FT                                thalassemia).
    FT                                /FTId=VAR_002847.
    FT   VARIANT     139    139       S -> P (in Attleboro; O(2) affinity up).
    FT                                /FTId=VAR_002848.
    FT   VARIANT     140    140       K -> E (in Hanamaki; O(2) affinity up).
    FT                                /FTId=VAR_002849.
    FT   VARIANT     140    140       K -> T (in Tokoname; O(2) affinity up).
    FT                                /FTId=VAR_002850.
    FT   VARIANT     141    141       Y -> H (in Rouen; O(2) affinity up).
    FT                                /FTId=VAR_002851.
    FT   VARIANT     142    142       R -> C (in Nunobiki; O(2) affinity up).
    FT                                /FTId=VAR_002852.
    FT   VARIANT     142    142       R -> H (in Suresnes; O(2) affinity up).
    FT                                /FTId=VAR_002854.
    FT   VARIANT     142    142       R -> L (in Legnano; O(2) affinity up).
    FT                                /FTId=VAR_002853.
    FT   VARIANT     142    142       R -> P (in Singapore).
    FT                                /FTId=VAR_002855.
    FT   HELIX         4     15
    FT   HELIX        16     20
    FT   HELIX        21     35
    FT   HELIX        37     42
    FT   HELIX        53     71
    FT   HELIX        73     75
    FT   HELIX        76     79
    FT   HELIX        81     89
    FT   HELIX        96    112
    FT   TURN        114    116
    FT   HELIX       119    136
    FT   TURN        137    139
    SQ   SEQUENCE   142 AA;  15258 MW;  15E13666573BBBAE CRC64;
         MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG
         KKVADALTNA VAHVDDMPNA LSALSDLHAH KLRVDPVNFK LLSHCLLVTL AAHLPAEFTP
         AVHASLDKFL ASVSTVLTSK YR
    //

## Output file format

An image is displayed on the specified graphics device.

### Output files for usage example

### Graphics File: pepwindow.ps

## Data files

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

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
    //

pepwindow can use any of the "Nakai et al." database of amino acid parameters - these used to be in a database called "NAKAI" but are now in one called "AAINDEX". EMBOSS has a program aaindexextract that takes data from this database and makes it available for pepwindow.

1. FTP the AAINDEX database from Japan:
ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1

2. Run aaindexextract with the aaindex1 file as input (or ask whoever installs EMBOSS to run it)

3. Run pepwindow with -datafile specifying the name of whatever "AAINDEX" datafile you wish to use. (Use embossdata -showall to see your available "AAINDEX" data file names.)

## 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

In calculating hydropathy, pepwindow 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).

## Diagnostic Error Messages

None.

## Exit status

0 upon successful completion.

## Known bugs

None.

## See also

Program name | Description
--- | ---
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq | Back-translate a protein sequence to a nucleotide sequence
charge | Draw a protein charge plot
checktrans | Reports STOP codons and ORF statistics of a protein
compseq | Calculate the composition of unique words in sequences
emowse | Search protein sequences by digest fragment molecular weight
freak | Generate residue/base frequency table or plot
iep | Calculate the isoelectric point of proteins
mwcontam | Find weights common to multiple molecular weights files
mwfilter | Filter noisy data from molecular weights file
octanol | Draw a White-Wimley protein hydropathy plot
pepinfo | Plot amino acid properties of a protein sequence in parallel
pepstats | Calculates statistics of protein properties
pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment
wordcount | Count and extract unique words in DNA sequence(s)

pepwindow can use any of the "Nakai et al." database of amino acid parameters - these are in a database called "AAINDEX". The program aaindexextract takes data from this database and makes it available for pepwindow.

## Author(s)

Ian Longden (il © sanger.ac.uk)
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Based on the original program by Jack Kyte and Russell F. Doolittle.

## History

Completed 27th May 1999.

## Target users

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

## Comments

None