Bio::Graphics::Glyph::translation - The "6-frame translation" glyph
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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.
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)
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
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)
Please report them.
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
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.
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.