EMBOSS: pepwindow


Program pepwindow

Function

Displays protein hydropathy

Description

Evaluation of protein hydropathy

Usage

Here is a sample session with pepwindow.

% pepwindow sw:hba_human

click here for result

Command line arguments

   Mandatory qualifiers:
  [-sequencea]         sequence   Sequence USA
   -graph              xygraph    Graph type

   Optional qualifiers:
   -datafile           datafile   nakai database file
   -length             integer    window size

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default
[-sequencea]
(Parameter 1)
Sequence USA Readable sequence Required
-graph Graph type EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm EMBOSS_GRAPHICS value, or x11
Optional qualifiers Allowed values Default
-datafile nakai database file Data file Enakai.dat
-length window size Integer from 1 to 200 7
Advanced qualifiers Allowed values Default
(none)

Input file format

Any protein sequence USA.

Output file format

.ps file if postscipt output requested.

Data files

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

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

Diagnostic Error Messages

Exit status

0 upon successfull completion.

Known bugs

See also

Program nameDescription
checktransReports STOP codons and ORF statistics of a protein sequence
digestProtein proteolytic enzyme or reagent cleavage digest
iepCalculates the isoelectric point of a protein
octanolDisplays protein hydropathy
pepinfoPlots simple amino acid properties in parallel
pepnetDisplays proteins as a helical net
pepstatsProtein statistics
pepwheelShows protein sequences as helices
pepwindowallDisplays protein hydropathy of a set of sequences

Author(s)

This application was written by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Based on 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