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
*  -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

   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
-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

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 nameDescription
abiviewReads ABI file and display the trace
cirdnaDraws circular maps of DNA constructs
garnierPredicts protein secondary structure
helixturnhelixReport nucleic acid binding motifs
hmomentHydrophobic moment calculation
lindnaDraws linear maps of DNA constructs
pepcoilPredicts coiled coil regions
pepnetDisplays proteins as a helical net
prettyplotDisplays aligned sequences, with colouring and boxing
prettyseqOutput sequence with translated ranges
remapDisplay a sequence with restriction cut sites, translation etc
seealsoFinds programs sharing group names
showalignDisplays a multiple sequence alignment
showdbDisplays information on the currently available databases
showfeatShow features of a sequence
showseqDisplay a sequence with features, translation etc
textsearchSearch sequence documentation text. SRS and Entrez are faster!
tmapDisplays 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.

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