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EMBOSS: pepwheel |
pepwheel
displays peptide sequences in a helical representation.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 Shows protein sequences as helices Graph type [x11]:
Mandatory qualifiers (* if not always prompted): [-sequence] sequence Sequence USA * -outfile outfile Output file name * -graph graph Graph type 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: -[no]wheel bool Plot the wheel -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'. -data bool Output the match data to a file instead of plotting it General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
-outfile | Output file name | Output file | <sequence>.pepwheel |
-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, png | EMBOSS_GRAPHICS value, or x11 |
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 | |
-[no]wheel | Plot the wheel | Yes/No | Yes |
-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 |
-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 |
---|---|
abiview | Reads ABI file and display the trace |
cirdna | Draws circular maps of DNA constructs |
garnier | Predicts protein secondary structure |
helixturnhelix | Report nucleic acid binding motifs |
hmoment | Hydrophobic moment calculation |
lindna | Draws linear maps of DNA constructs |
pepcoil | Predicts coiled coil regions |
pepnet | Displays proteins as a helical net |
prettyplot | Displays aligned sequences, with colouring and boxing |
prettyseq | Output sequence with translated ranges |
remap | Display a sequence with restriction cut sites, translation etc |
seealso | Finds programs sharing group names |
showalign | Displays a multiple sequence alignment |
showdb | Displays information on the currently available databases |
showfeat | Show features of a sequence |
showseq | Display a sequence with features, translation etc |
textsearch | Search sequence documentation text. SRS and Entrez are faster! |
tmap | Displays membrane spanning regions |