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:6.5.0.0

   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

[pepwindowall results]

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:

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