
                               pepwindowall 



Function

   Draw Kyte-Doolittle hydropathy plot for a protein alignment

Description

   pepwindow draws a set of superimposed Kyte & Doolittle hydropathy
   plots for a set of protein sequences.

Algorithm

   pepwindow 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

   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, 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: "-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 -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. 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

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: 0.61
  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

   An image is displayed on the specified graphics device.

  Output files for usage example

  Graphics File: pepwindowall.ps

   [pepwindowall results]

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

   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 pepwindow, 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
   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
   pepwindow Draw a Kyte-Doolittle hydropathy plot for a protein sequence
   wordcount Count and extract unique words in DNA sequence(s)

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
