Bio::Graphics::Glyph::translation.3pm

Langue: en

Version: 2009-06-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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.