Bio::Graphics::DrawTransmembrane man page on Pidora

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Bio::Graphics::DrawTraUsermContributed PerlBio::Graphics::DrawTransmembrane(3)

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>

perl v5.14.1			  2011-07-2Bio::Graphics::DrawTransmembrane(3)
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