man Bio::Graphics::Glyph::translation (3): The 6-frame translation glyph

SYNOPSIS

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

DESCRIPTION

This glyph draws the conceptual translation of DNA sequences. At high magnifications, it simply draws lines indicating open reading frames. At low magnifications, it draws a conceptual protein translation. Options can be used to set 1-frame, 3-frame or 6-frame translations.

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
  ------        -----------                 -------
  -translation  Type of translation to      1frame
                perform.  One of "1frame",
                "3frame", or "6frame"
  -strand       Forward (+1) or reverse (-1) +1
                translation.
  -frame0       Color for the first frame    fgcolor
  -frame1       Color for the second frame   fgcolor
  -frame2       Color for the third frame    fgcolor
  -gridcolor    Color for the horizontal     lightgrey
                lines of the reading frames
  -start_codons Draw little arrowheads       0 (false)
                indicating start codons
  -stop_codons  Draw little vertical ticks   1 (true)
                indicating stop codons
  -arrow_height Height of the start codon    1
                arrowheads
  -show_sequence Show the amino acid sequence 1 (true)
                if there's room.
  -triletter_code Show the 3-letter amino acid 0 (false)
                code if there's room
  -codontable   Codon table to use           1 (see Bio::Tools::CodonTable)

SUGGESTED STANZA FOR GENOME BROWSER

This produces a nice gbrowse display in which the DNA/GC Content glyph is sandwiched between the forward and reverse three-frame translations. The frames are color-coordinated with the example configuration for the ``cds'' glyph.

 [TranslationF]
 glyph        = translation
 global feature = 1
 frame0       = cadetblue
 frame1       = blue
 frame2       = darkblue
 height       = 20
 fgcolor      = purple
 strand       = +1
 translation  = 3frame
 key          = 3-frame translation (forward)
 [DNA/GC Content]
 glyph        = dna
 global feature = 1
 height       = 40
 do_gc        = 1
 fgcolor      = red
 axis_color   = blue
 [TranslationR]
 glyph        = translation
 global feature = 1
 frame0       = darkred
 frame1       = red
 frame2       = crimson
 height       = 20
 fgcolor      = blue
 strand       = -1
 translation  = 3frame
 key          = 3-frame translation (reverse)

BUGS

Please report them.

AUTHOR

Lincoln Stein <[email protected]>.