---
name: "Bio::Graphics::Glyph::protein"
section: "3pm"
platform: "linux"
package: "libbio-graphics-perl"
version: "2.40-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Graphics::Glyph::protein"
---

# Bio::Graphics::Glyph::protein(3pm)

The "protein" glyph

## NAME

Bio::Graphics::Glyph::protein - The "protein" glyph

## SYNOPSIS

```
  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
```

## DESCRIPTION

This glyph draws protein sequences.  At high magnifications, this glyph will draw the actual amino acids of the sequence.  At low magnifications, the glyph will plot the Kyte-Doolite hydropathy.  By default, the KD plot will use a window size of 9 residues, but this can be changed by specifying the kd\_window option.

The feature may return either a protein sequence or a DNA sequence in response to the **seq()** method. However, if it returns a DNA sequence, then the feature must also return the correct phase and strand in order for the glyph to translate its open reading frame correctly!

### OPTIONS

The following options are standard among all Glyphs.  See Bio::Graphics::Glyph for a full explanation.

```
  Option      Description                      Default
  ------      -----------                      -------
  -fgcolor      Foreground color               black
  -outlinecolor Synonym for -fgcolor
  -bgcolor      Background color               turquoise
  -fillcolor    Synonym for -bgcolor
  -linewidth    Line width                     1
  -height       Height of glyph                10
  -font         Glyph font                     gdSmallFont
  -connector    Connector type                 0 (false)
  -connector_color
                Connector color                black
  -label        Whether to draw a label        0 (false)
  -description  Whether to draw a description  0 (false)
  -hilite       Highlight color                undef (no color)
```

In addition to the common options, the following glyph-specific options are recognized:

```
  Option      Description               Default
  ------      -----------               -------
  -do_kd      Whether to draw the Kyte-  true
              Doolittle hydropathy plot
              at low mags
  -kd_window  Size of the sliding window  9
              to use in the KD hydropathy
              calculation.
  -axis_color Color of the vertical axes  fgcolor
              in the KD hydropathy plot
  -phase_style  The way phase is to be
                interpreted. One of            "012"
                "012" or "021"
```

## BUGS

Please report them.

## SEE ALSO

Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::extending\_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded\_segments, Bio::Graphics::Glyph::heterogeneous\_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler\_arrow, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD

## AUTHOR

Aaron J. Mackey, based on the "dna" glyphy by Lincoln Stein \<lstein@cshl.org\> and Peter Ashton \<pda@sanger.ac.uk\>.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.  See DISCLAIMER.txt for disclaimers of warranty.