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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Graphics::DrawTransmembrane \- draw a cartoon of an Alpha\-helical transmembrane protein. .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 2 \& 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 => \*(AqThis is a cartoon displaying transmembrane helices.\*(Aq, \& \-topology => \e@topology); \& \& ## More advanced use \& my %labels = (5 => \*(Aq5 \- Sulphation Site\*(Aq, \& 21 => \*(Aq1st Helix\*(Aq, \& 47 => \*(Aq40 \- Mutation\*(Aq, \& 60 => \*(AqVoltage Sensor\*(Aq, \& 72 => \*(Aq72 \- Mutation 2\*(Aq, \& 73 => \*(Aq73 \- Mutation 3\*(Aq, \& 138 => \*(Aq138 \- Glycosylation Site\*(Aq, \& 170 => \*(Aq170 \- Phosphorylation Site\*(Aq, \& 200 => \*(AqLast Helix\*(Aq); \& \& my $im = Bio::Graphics::DrawTransmembrane\->new(\-n_terminal=> \*(Aqout\*(Aq, \& \-topology => \e@topology, \& \-bold_helices=> 1, \& \-labels=> \e%labels, \& \-text_offset=> \-15, \& \-outside_label=>\*(AqLumen\*(Aq, \& \-inside_label=>\*(AqCytoplasm\*(Aq, \& \-membrane_label=>\*(AqMembrane\*(Aq, \& \-vertical_padding=> 155); \& \& ## Parse Tmhmm data \& use Bio::Tools::Tmhmm; \& my $im = Bio::Graphics::DrawTransmembrane\->new( \& \-title=>\*(AqLet\e\*(Aqs parse some Tmhmm output...\*(Aq, \& \-bold_helices=> 1); \& open(FILE, \*(Aqtmhmm.out\*(Aq); \& my $parser = new Bio::Tools::Tmhmm(\-fh => \e*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; .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" A module to draw a cartoon of an alpha-helical transmembrane protein. It uses \s-1GD\s0 and allows the image to be written to a .png file. .PP The options are a set of tag/value pairs as follows: .PP .Vb 2 \& 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 \*(Aqin\*(Aq or \*(Aqout\*(Aq \& \& \-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 => \*(AqGlycosylation Site\*(Aq, \& 190 => \*(AqBinding Site\*(Aq); \& \& 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 \*(AqS\*(Aq 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\*(Aqt 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 .Ve .PP 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. .SH "AUTHOR" .IX Header "AUTHOR" Tim Nugent