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EMBOSS: pepwheel |
This gives a view of a helix from a protein sequence looking down the axis of the helix.
It is useful for highlighting amphipathicity and other properties of residues around a helix.
% pepwheel sw:hbb_human -send 30 Graph type [xwin]:click here for result
Mandatory qualifiers (* if not always prompted): [-sequence] sequence Sequence USA * -graph graph Graph type * -outfile outfile Output file name Optional qualifiers (* if not always prompted): -steps integer The number of residues plotted per turn is this value divided by the 'turns' value. -turns integer The number of residues plotted per turn is the 'steps' value divided by this value. * -squares string By default the aliphatic residues ILVM are marked with squares. * -diamonds string By default the residues DENQST are marked with diamonds. * -octags string By default the positively charged residues HKR are marked with octagons. Advanced qualifiers: -amphipathic bool If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified using the qualifiers '-squares', '-diamonds' and '-octags'. -[no]wheel bool Plot the wheel -data bool Output the match data to a file instead of plotting it |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (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 |
-outfile | Output file name | Output file | <sequence>.pepwheel |
Optional qualifiers | Allowed values | Default | |
-steps | The number of residues plotted per turn is this value divided by the 'turns' value. | Integer from 2 to 100 | 18 |
-turns | The number of residues plotted per turn is the 'steps' value divided by this value. | Integer from 1 to 100 | 5 |
-squares | By default the aliphatic residues ILVM are marked with squares. | Any string is accepted | ILVM |
-diamonds | By default the residues DENQST are marked with diamonds. | Any string is accepted | DENQST |
-octags | By default the positively charged residues HKR are marked with octagons. | Any string is accepted | HKR |
Advanced qualifiers | Allowed values | Default | |
-amphipathic | If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified using the qualifiers '-squares', '-diamonds' and '-octags'. | Yes/No | No |
-[no]wheel | Plot the wheel | Yes/No | Yes |
-data | Output the match data to a file instead of plotting it | Yes/No | No |
helix phi psi omega res/turn transl. turns steps alpha -57 -47 180 3.6 1.50 5 18 3-10 -49 -26 180 3.0 2.00 1 3 pi -57 -70 180 4.4 1.15 5 22 PP I -83 158 0 3.33 1.9 3 10 PP II -78 149 180 3.0 3.12 1 3 PG II -80 150 180 3.0 3.1 1 3 anti Beta -139 135 -178 2.0 3.4 4 9 para Beta -119 113 180 2.0 3.2 4 9 PP is polyproline PG II is polyGlycine.
Program name | Description |
---|---|
checktrans | Reports STOP codons and ORF statistics of a protein sequence |
digest | Protein proteolytic enzyme or reagent cleavage digest |
garnier | Predicts protein secondary structure |
helixturnhelix | Report nucleic acid binding motifs |
iep | Calculates the isoelectric point of a protein |
octanol | Displays protein hydropathy |
pepcoil | Predicts coiled coil regions |
pepinfo | Plots simple amino acid properties in parallel |
pepnet | Displays proteins as a helical net |
pepstats | Protein statistics |
pepwindow | Displays protein hydropathy |
pepwindowall | Displays protein hydropathy of a set of sequences |
sigcleave | Reports protein signal cleavage sites |