Lincoln D. Stein > Bio-Graphics-2.32 > Bio::Graphics::DrawTransmembrane

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NAME ^

Bio::Graphics::DrawTransmembrane - draw a cartoon of an Alpha-helical transmembrane protein.

SYNOPSIS ^

  use Bio::Graphics::DrawTransmembrane;
  my @topology = (20,45,59,70,86,109,145,168,194,220);

  ## Simple use - -topology is the only option that is required

  my $im = Bio::Graphics::DrawTransmembrane->new(
      -title => 'This is a cartoon displaying transmembrane helices.',
      -topology => \@topology);

  ## More advanced use
  my %labels = (5 => '5 - Sulphation Site',
                21 => '1st Helix',
                47 => '40 - Mutation',
                60 => 'Voltage Sensor',
                72 => '72 - Mutation 2',
                73 => '73 - Mutation 3',
                138 => '138 - Glycosylation Site',
                170 => '170 - Phosphorylation Site',
                200 => 'Last Helix');

  my $im = Bio::Graphics::DrawTransmembrane->new(-n_terminal=> 'out',
                                  -topology => \@topology,
                                  -bold_helices=> 1,
                                  -labels=> \%labels,
                                  -text_offset=> -15,
                                  -outside_label=>'Lumen',
                                  -inside_label=>'Cytoplasm',
                                  -membrane_label=>'Membrane',
                                  -vertical_padding=> 155);

  ## Parse Tmhmm data
  use Bio::Tools::Tmhmm;
  my $im = Bio::Graphics::DrawTransmembrane->new(
      -title=>'Let\'s parse some Tmhmm output...',
      -bold_helices=> 1);
  open(FILE, 'tmhmm.out');
  my $parser = new Bio::Tools::Tmhmm(-fh => \*FILE );
  while(my $tmhmm_feat = $parser->next_result ) {
        ## Load features into DrawTransmembrane object
        $im->add_tmhmm_feat($tmhmm_feat);
  }
  close FILE;

  ## Now write the image to a .png file
  open(OUTPUT, ">output.png");
  binmode OUTPUT;
  print OUTPUT $im->png;
  close OUTPUT;

DESCRIPTION ^

A module to draw a cartoon of an alpha-helical transmembrane protein. It uses GD and allows the image to be written to a .png file.

The options are a set of tag/value pairs as follows:

  Option              Value                                         Default
  ------              -----                                         -------

  -topology           Array containing transmembrane helix          none
                      boundaries. This is the only option that 
                      is required

  -topology_string    Alternative to -topology, provide a string    none
                      containing the topology data in the form
                      A.11,31;B.41,59;C.86,107;D.145,166

  -n_terminal         Location of the N-terminal of the sequence,   out
                      either 'in' or 'out'

  -title              Title to add to the image                     none

  -inside_label       Label for the inside of the membrane          Cytoplasmic

  -outside_label      Label for the outside of the membrane         Extracellular

  -membrane_label     Label for the membrane                        Plasma Membrane

  -colour_scheme      Colour scheme to use. Current choices are     blue
                      blue, yellow, red, green, pink or white. 

  -labels             Label loops and helices using data from a     none
                      hash, e.g.

                      %labels = (138 => 'Glycosylation Site',
                                 190 => 'Binding Site');

                      The hash key must be numeric, ranges are 
                      not allowed.

  -bold_helices       Draws black boxes round helices               1

  -bold_labels        Draws black boxes round labels                0

  -text_offset        Shift the text labeling the loops. Use a      0 
                      negative value to shift it left, a positive
                      value to shift it right

  -helix_height       Transmembrane helix height                    130

  -helix_width        Transmembrane helix width                     50

  -loop_width         Loop width                                    20

  -vertical_padding   Vertical padding                              140

  -horizontal_padding Horizontal Padding                            150

  -membrane_offset    Offest between helix end and membrane         6

  -short_loop_height  Height of short loops                         90

  -medium_loop_height Height of medium loops                        120

  -long_loop_height   Height of long loops                          150

  -short_loop_limit   Length in residues below which a loop is      15
                      classed as short

  -long_loop_limit    Length in residues above which a loop is      30
                      classed as long

  -loop_heights       Explicitly set heights of each loop, e.g.

                      %loop_heights = (1 => 45,
                                       2 => 220,
                                       3 => 50,
                                       4 => 220,
                                       9 => 70);

                      The key corresponds to the loop number. Both
                      key and value must be numeric. If you use
                      -loop_height and there is a defined height
                      for the current loop then other height values
                      will be overridden

  -n_terminal_height  Height of N-terminal                          150

  -c_terminal_height  Height of C-terminal                          80

  -n_terminal_offset  Shift the N-terminal left by this amount      0

  -c_terminal_offset  Shift the C-terminal right by this amount     0

  -helix_label        Change the 'S' label on each helix. Only 1    S
                      character is allowed

  -show_labels        Display text labels                           on

  -draw_cytosol       Show the cytosol                              false

  -draw_bilayer       Show the membrane                             true

  -draw_loops         Show the loops                                true

  -draw_terminai      Show the terminai                             true

  -draw_helices       Show the helices                              true

  -dontsort           Don't automatically sort the topology array   0

  -ttf_font           Path to TTF font, e.g.                        none 
                      /usr/share/fonts/msttcorefonts/arial.ttf

  -ttf_font_size      Default size for TTF font. Use 7-9 with       8
                      Arial for best results  

Height, width, padding and other numerical values can gernerally be left alone. They are useful if your labels consists of a lot of text as this may lead to them overlapping. In this case try increasing the loop_width or helix_width options. -text_offset is also very useful for avoiding overlapping.

AUTHOR ^

Tim Nugent <timnugent@gmail.com>

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