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Inputting info
01-17-2012
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Bio::Graphics::Glyph::translation(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::translation(3pm) 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 v5.14.2 2012-02-20 Bio::Graphics::Glyph::translation(3pm)