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.
-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.