| 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 tsw:hbb_human -send 30
    Shows protein sequences as helices
    Graph type [x11]: cps

    Created pepwheel.ps

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          sequence   Protein sequence filename and optional
                                      format, or reference (input USA)
       -graph              graph      [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tekt, tek, none, data, xterm, png, gif)

       Additional (Optional) qualifiers (* if not always prompted):
       -steps              integer    [18] The number of residues plotted per turn
                                      is this value divided by the 'turns' value.
                                      (Integer from 2 to 100)
       -turns              integer    [5] The number of residues plotted per turn
                                      is the 'steps' value divided by this value.
                                      (Integer from 1 to 100)
    *  -squares            string     [ILVM] By default the aliphatic residues
                                      ILVM are marked with squares. (Any string is
                                      accepted)
    *  -diamonds           string     [DENQST] By default the residues DENQST are
                                      marked with diamonds. (Any string is
                                      accepted)
    *  -octags             string     [HKR] By default the positively charged
                                      residues HKR are marked with octagons. (Any
                                      string is accepted)

       Advanced (Unprompted) qualifiers:
       -[no]wheel          boolean    [Y] Plot the wheel
       -amphipathic        toggle     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'.

       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of the sequence to be used
       -send1              integer    End of the sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-graph" associated qualifiers
       -gprompt            boolean    Graph prompting
       -gdesc              string     Graph description
       -gtitle             string     Graph title
       -gsubtitle          string     Graph subtitle
       -gxtitle            string     Graph x axis title
       -gytitle            string     Graph y axis title
       -goutfile           string     Output file for non interactive displays
       -gdirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write standard output
       -filter             boolean    Read standard input, write standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Protein sequence filename and optional format, or reference (input USA) | Readable sequence | Required
-graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
Additional (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 (Unprompted) qualifiers | Allowed values | Default
-[no]wheel | Plot the wheel | Boolean value 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'. | Toggle value Yes/No | No

## Input file format

pepwheel reads any protein sequence USA.

### Input files for usage example

'tsw:hbb_human' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:hbb_human

    ID   HBB_HUMAN               Reviewed;         147 AA.
    AC   P68871; P02023; Q13852; Q14481; Q14510; Q45KT0; Q6FI08; Q8IZI1;
    AC   Q9BX96; Q9UCP8; Q9UCP9;
    DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
    DT   23-JAN-2007, sequence version 2.
    DT   20-MAR-2007, entry version 43.
    DE   Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin).
    GN   Name=HBB;
    OS   Homo sapiens (Human).
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
    OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
    OC   Catarrhini; Hominidae; Homo.
    OX   NCBI_TaxID=9606;
    RN   [1]
    RP   NUCLEOTIDE SEQUENCE.
    RX   MEDLINE=81064667; PubMed=6254664; DOI=10.1016/0092-8674(80)90428-6;
    RA   Lawn R.M., Efstratiadis A., O'Connell C., Maniatis T.;
    RT   "The nucleotide sequence of the human beta-globin gene.";
    RL   Cell 21:647-651(1980).
    RN   [2]
    RP   NUCLEOTIDE SEQUENCE.
    RX   MEDLINE=77126403; PubMed=1019344;
    RA   Marotta C., Forget B., Cohen-Solal M., Weissman S.M.;
    RT   "Nucleotide sequence analysis of coding and noncoding regions of human
    RT   beta-globin mRNA.";
    RL   Prog. Nucleic Acid Res. Mol. Biol. 19:165-175(1976).
    RN   [3]
    RP   NUCLEOTIDE SEQUENCE.
    RA   Lu L., Hu Z.H., Du C.S., Fu Y.S.;
    RT   "DNA sequence of the human beta-globin gene isolated from a healthy
    RT   Chinese.";
    RL   Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
    RN   [4]
    RP   NUCLEOTIDE SEQUENCE, AND VARIANT DURHAM-N.C. PRO-115.
    RC   TISSUE=Blood;
    RA   Kutlar F., Abboud M., Leithner C., Holley L., Brisco J., Kutlar A.;
    RT   "Electrophoretically silent, very unstable, thalassemic mutation at
    RT   codon 114 of beta globin (hemoglobin Durham-N.C.) detected by cDNA
    RT   sequencing of mRNA, from a Russian women.";
    RL   Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
    RN   [5]
    RP   NUCLEOTIDE SEQUENCE, AND VARIANT LOUISVILLE LEU-43.
    RC   TISSUE=Blood;
    RA   Kutlar F., Harbin J., Brisco J., Kutlar A.;
    RT   "Rapid detection of electrophoretically silent, unstable human
    RT   hemoglobin 'Louisville', (Beta; Phe 42 Leu/TTT to CTT) by cDNA
    RT   sequencing of mRNA.";
    RL   Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases.
    RN   [6]
    RP   NUCLEOTIDE SEQUENCE, AND VARIANT TY GARD GLN-125.

      [Part of this file has been deleted for brevity]

    FT   VARIANT     141    141       A -> T (in St Jacques: O(2) affinity up).
    FT                                /FTId=VAR_003081.
    FT   VARIANT     141    141       A -> V (in Puttelange; polycythemia; O(2)
    FT                                affinity up).
    FT                                /FTId=VAR_003082.
    FT   VARIANT     142    142       L -> R (in Olmsted; unstable).
    FT                                /FTId=VAR_003083.
    FT   VARIANT     143    143       A -> D (in Ohio; O(2) affinity up).
    FT                                /FTId=VAR_003084.
    FT   VARIANT     144    144       H -> D (in Rancho Mirage).
    FT                                /FTId=VAR_003085.
    FT   VARIANT     144    144       H -> P (in Syracuse; O(2) affinity up).
    FT                                /FTId=VAR_003087.
    FT   VARIANT     144    144       H -> Q (in Little Rock; O(2) affinity
    FT                                up).
    FT                                /FTId=VAR_003086.
    FT   VARIANT     144    144       H -> R (in Abruzzo; O(2) affinity up).
    FT                                /FTId=VAR_003088.
    FT   VARIANT     145    145       K -> E (in Mito; O(2) affinity up).
    FT                                /FTId=VAR_003089.
    FT   VARIANT     146    146       Y -> C (in Rainier; O(2) affinity up).
    FT                                /FTId=VAR_003090.
    FT   VARIANT     146    146       Y -> H (in Bethesda; O(2) affinity up).
    FT                                /FTId=VAR_003091.
    FT   VARIANT     147    147       H -> D (in Hiroshima; O(2) affinity up).
    FT                                /FTId=VAR_003092.
    FT   VARIANT     147    147       H -> L (in Cowtown; O(2) affinity up).
    FT                                /FTId=VAR_003093.
    FT   VARIANT     147    147       H -> P (in York; O(2) affinity up).
    FT                                /FTId=VAR_003094.
    FT   VARIANT     147    147       H -> Q (in Kodaira; O(2) affinity up).
    FT                                /FTId=VAR_003095.
    FT   HELIX         5     15
    FT   TURN         20     22
    FT   HELIX        23     34
    FT   HELIX        36     41
    FT   HELIX        43     45
    FT   HELIX        51     56
    FT   HELIX        58     76
    FT   TURN         77     79
    FT   HELIX        81     93
    FT   TURN         94     96
    FT   HELIX       101    118
    FT   HELIX       119    121
    FT   HELIX       124    141
    FT   HELIX       143    145
    SQ   SEQUENCE   147 AA;  15998 MW;  A31F6D621C6556A1 CRC64;
         MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
         VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
         KEFTPPVQAA YQKVVAGVAN ALAHKYH
    //

## Output file format

An image is output to the specified graphics device.

### Output files for usage example

### Graphics File: pepwheel.ps

## 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 sequence with restriction 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
sixpack | Display a DNA sequence with 6-frame translation and ORFs
textsearch | Search sequence documentation. Slow, use SRS and Entrez!
tmap | Displays membrane spanning regions

## Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## History

Written (March 1999) - Alan Bleasby

## Target users

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

## Comments

None