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EMBOSS: pepwindowall |
It is useful for visualising the average hydropathy and its variability along the alignment.
% pepwindowall globin.msf -gxtitle="Base Number" -gytitle="hydropathy"click here for result
Mandatory qualifiers: [-msf] seqset File containing a sequence alignment [-graph] xygraph Graph type Optional qualifiers: -datafile datafile nakai database file -length integer window size Advanced qualifiers: (none) |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-msf] (Parameter 1) |
File containing a sequence alignment | Readable sequences | Required |
[-graph] (Parameter 2) |
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) |
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 //
Program name | Description |
---|---|
checktrans | Reports STOP codons and ORF statistics of a protein sequence |
digest | Protein proteolytic enzyme or reagent cleavage digest |
iep | Calculates the isoelectric point of a protein |
octanol | Displays protein hydropathy |
pepinfo | Plots simple amino acid properties in parallel |
pepnet | Displays proteins as a helical net |
pepstats | Protein statistics |
pepwheel | Shows protein sequences as helices |
pepwindow | Displays protein hydropathy |
Completed 4th June 1999.