Bio::Graphics::Glyph::translation - The "6-frame translation" glyph

- NAME
- SYNOPSIS
- DESCRIPTION

- OPTIONS

- SUGGESTED STANZA FOR GENOME BROWSER
- BUGS
- SEE ALSO
- AUTHOR

# 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 the Bio::Graphics::Glyph manpage 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

the Bio::Graphics::Panel manpage, the Bio::Graphics::Glyph manpage, the Bio::Graphics::Glyph::arrow manpage, the Bio::Graphics::Glyph::cds manpage, the Bio::Graphics::Glyph::crossbox manpage, the Bio::Graphics::Glyph::diamond manpage, the Bio::Graphics::Glyph::dna manpage, the Bio::Graphics::Glyph::dot manpage, the Bio::Graphics::Glyph::ellipse manpage, the Bio::Graphics::Glyph::extending_arrow manpage, the Bio::Graphics::Glyph::generic manpage, the Bio::Graphics::Glyph::graded_segments manpage, the Bio::Graphics::Glyph::heterogeneous_segments manpage, the Bio::Graphics::Glyph::line manpage, the Bio::Graphics::Glyph::pinsertion manpage, the Bio::Graphics::Glyph::primers manpage, the Bio::Graphics::Glyph::rndrect manpage, the Bio::Graphics::Glyph::segments manpage, the Bio::Graphics::Glyph::ruler_arrow manpage, the Bio::Graphics::Glyph::toomany manpage, the Bio::Graphics::Glyph::transcript manpage, the Bio::Graphics::Glyph::transcript2 manpage, the Bio::Graphics::Glyph::translation manpage, the Bio::Graphics::Glyph::triangle manpage, the Bio::DB::GFF manpage, the Bio::SeqI manpage, the Bio::SeqFeatureI manpage, the Bio::Das manpage, 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.

Bio::Graphics::Glyph::translation - The "6-frame translation" glyph