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Bio::Graphics::Glyph::UsersContributed PerBio::Graphics::Glyph::translation(3)

NAME
       Bio::Graphics::Glyph::translation - 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.

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
       Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2001 Cold Spring Harbor Laboratory

       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.

perl v5.32.1			  2021-11-Bio::Graphics::Glyph::translation(3)

NAME | SYNOPSIS | DESCRIPTION | SUGGESTED STANZA FOR GENOME BROWSER | BUGS | SEE ALSO | AUTHOR

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