Lincoln D. Stein > Bio-Graphics-2.32 > Bio::Graphics::Glyph::translation

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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.

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