| ## EMBOSS: pepwheel

# Program pepwheel

## Function

Shows protein sequences as helices

## Description

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.

## Usage

Here is a sample session with pepwheel.

    % pepwheel sw:hbb_human -send 30
    Shows protein sequences as helices
    Graph type [x11]:

click here for result

## Command line arguments

       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

## Input file format

Any protein sequence USA.

## Output file format

An image is output.

## Data files

None.

## Notes

The default settings for turn (5) and steps (18) apply to alpha helices. For other possible secondary structures, see the following table:

    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.

## References

1. Rachamandran and Sasisekharan, Adv. Protein Chem. 23:283-437, 1968
2. IUPAC-IUB Commission on biochemical nomenclature, Biochemistry 9:3471-3479, 1970

## Warnings

When you specify the number of turns and steps, be aware that you should remove common factors from these two numbers. For example, if you (for some improbable reason) wished to plot a wheel with 8 turns in 18 steps (2.25 residues per turn) you should remove the common factor (i.e. 2) and specify 4 turns in 9 steps.

## Diagnostic Error Messages

None.

## Exit status

0 upon successful completion.

## Known bugs

None.

## See also

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

## Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

## History

Writte (March 1999) - Alan Bleasby

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments