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pepwindowall |
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pepwindowall draws a set of superimposed Kyte & Doolittle hydropathy plots for a set of alignedprotein sequences.
pepwindowall calculates hydropathy in windows of a specified size over the input sequences.
% 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
Draw Kyte-Doolittle hydropathy plot for a protein alignment
Version: EMBOSS:6.4.0.0
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
-length 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
-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 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 |
| -length | 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 |
| -sformat1 -sformat_sequences |
string | Input sequence format | Any string | |
| -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 | |
| -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 |
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.
!!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~~~
|
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.
![[pepwindowall results]](pepwindowall.1.pepwindowall.gif)
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
//
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.
| 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 | Calculates statistics of protein properties |
| pepwindow | Draw a hydropathy plot for a protein sequence |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.