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EMBOSS: pepnet |
It is therefore easy to see patterns of amphipathicity that you may wish to investigate in more detail by using displays such as pepwheel.
You can specify which residues to mark up in squares, diamonds and octagons.
% pepnet -sask
Input sequence: sw:gcn4_yeast
Begin at position [start]: 253
End at position [end]: 274
Graph type [x11]:
Mandatory qualifiers (* if not always prompted):
[-sequence] sequence Sequence USA
* -graph graph Graph type
Optional qualifiers (* if not always prompted):
* -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'.
-data bool Output the 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 |
| -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 | |
| -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 |
| -data | Output the data to a file instead of plotting it | Yes/No | No |
| 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 |
| pepwheel | Shows protein sequences as helices |
| 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 |
