Difference between revisions of "AminoAcidColours.pl"

From Organic Design wiki
m
(Adding useful lookup tables)
Line 147: Line 147:
  
 
${$params->{'motif'}} =~ s/([@{[join "",keys %{$residue_color_schemes ->{$params->{schema}}}]}])/<font color=\"$residue_color_schemes->{$params->{schema}}->{$1}\" class="est">$1<\/font>/g;
 
${$params->{'motif'}} =~ s/([@{[join "",keys %{$residue_color_schemes ->{$params->{schema}}}]}])/<font color=\"$residue_color_schemes->{$params->{schema}}->{$1}\" class="est">$1<\/font>/g;
 +
}
 +
 +
 +
# ------------------------- Other useful lookup tables -------------------------- #
 +
# Source: http://examples.oreilly.com/begperlbio/
  
−
}
+
 
 +
    my %three2one = (
 +
      'ALA' => 'A',
 +
      'VAL' => 'V',
 +
      'LEU' => 'L',
 +
      'ILE' => 'I',
 +
      'PRO' => 'P',
 +
      'TRP' => 'W',
 +
      'PHE' => 'F',
 +
      'MET' => 'M',
 +
      'GLY' => 'G',
 +
      'SER' => 'S',
 +
      'THR' => 'T',
 +
      'TYR' => 'Y',
 +
      'CYS' => 'C',
 +
      'ASN' => 'N',
 +
      'GLN' => 'Q',
 +
      'LYS' => 'K',
 +
      'ARG' => 'R',
 +
      'HIS' => 'H',
 +
      'ASP' => 'D',
 +
      'GLU' => 'E',
 +
    );
 +
 
 +
my(%genetic_code) = (
 +
   
 +
    'TCA' => 'S',    # Serine
 +
    'TCC' => 'S',    # Serine
 +
    'TCG' => 'S',    # Serine
 +
    'TCT' => 'S',    # Serine
 +
    'TTC' => 'F',    # Phenylalanine
 +
    'TTT' => 'F',    # Phenylalanine
 +
    'TTA' => 'L',    # Leucine
 +
    'TTG' => 'L',    # Leucine
 +
    'TAC' => 'Y',    # Tyrosine
 +
    'TAT' => 'Y',    # Tyrosine
 +
    'TAA' => '_',    # Stop
 +
    'TAG' => '_',    # Stop
 +
    'TGC' => 'C',    # Cysteine
 +
    'TGT' => 'C',    # Cysteine
 +
    'TGA' => '_',    # Stop
 +
    'TGG' => 'W',    # Tryptophan
 +
    'CTA' => 'L',    # Leucine
 +
    'CTC' => 'L',    # Leucine
 +
    'CTG' => 'L',    # Leucine
 +
    'CTT' => 'L',    # Leucine
 +
    'CCA' => 'P',    # Proline
 +
    'CCC' => 'P',    # Proline
 +
    'CCG' => 'P',    # Proline
 +
    'CCT' => 'P',    # Proline
 +
    'CAC' => 'H',    # Histidine
 +
    'CAT' => 'H',    # Histidine
 +
    'CAA' => 'Q',    # Glutamine
 +
    'CAG' => 'Q',    # Glutamine
 +
    'CGA' => 'R',    # Arginine
 +
    'CGC' => 'R',    # Arginine
 +
    'CGG' => 'R',    # Arginine
 +
    'CGT' => 'R',    # Arginine
 +
    'ATA' => 'I',    # Isoleucine
 +
    'ATC' => 'I',    # Isoleucine
 +
    'ATT' => 'I',    # Isoleucine
 +
    'ATG' => 'M',    # Methionine
 +
    'ACA' => 'T',    # Threonine
 +
    'ACC' => 'T',    # Threonine
 +
    'ACG' => 'T',    # Threonine
 +
    'ACT' => 'T',    # Threonine
 +
    'AAC' => 'N',    # Asparagine
 +
    'AAT' => 'N',    # Asparagine
 +
    'AAA' => 'K',    # Lysine
 +
    'AAG' => 'K',    # Lysine
 +
    'AGC' => 'S',    # Serine
 +
    'AGT' => 'S',    # Serine
 +
    'AGA' => 'R',    # Arginine
 +
    'AGG' => 'R',    # Arginine
 +
    'GTA' => 'V',    # Valine
 +
    'GTC' => 'V',    # Valine
 +
    'GTG' => 'V',    # Valine
 +
    'GTT' => 'V',    # Valine
 +
    'GCA' => 'A',    # Alanine
 +
    'GCC' => 'A',    # Alanine
 +
    'GCG' => 'A',    # Alanine
 +
    'GCT' => 'A',    # Alanine
 +
    'GAC' => 'D',    # Aspartic Acid
 +
    'GAT' => 'D',    # Aspartic Acid
 +
    'GAA' => 'E',    # Glutamic Acid
 +
    'GAG' => 'E',    # Glutamic Acid
 +
    'GGA' => 'G',    # Glycine
 +
    'GGC' => 'G',    # Glycine
 +
    'GGG' => 'G',    # Glycine
 +
    'GGT' => 'G',    # Glycine
 +
    );
 +
 
 +
my %iub2character_class = (
 +
   
 +
        A => 'A',
 +
        C => 'C',
 +
        G => 'G',
 +
        T => 'T',
 +
        R => '[GA]',
 +
        Y => '[CT]',
 +
        M => '[AC]',
 +
        K => '[GT]',
 +
        S => '[GC]',
 +
        W => '[AT]',
 +
        B => '[CGT]',
 +
        D => '[AGT]',
 +
        H => '[ACT]',
 +
        V => '[ACG]',
 +
        N => '[ACGT]',
 +
    );

Revision as of 19:51, 24 May 2007

  1. {{#Security: *|Sven}}Our Perl scripts.

sub colorise_peptide { 

   my $params = {motif => ,

schema => $form_data{"-schema"} || 'accessible_area', blocks => 0, start => 1, @_}; 

   unless(ref $params->{'motif'} eq 'SCALAR')
   {

&return_html_error('title_text' => 'INTERNAL ERROR', 'error_msg' => qq|&nucleotide_colors subroutine variable 'motif' requires a SCALAR reference as input|); exit 0; 

   }  
   
   my $residue_color_schemes =
   {
       'accessible_area' =>
       {

'C' => '#FF66FF', # pink 'I' => '#FF3300', # red 'G' => '#FF3300', # red 'V' => '#FF3300', # red 'A' => '#9900CC', # purple 'F' => '#9900CC', # purple 'L' => '#9900CC', # purple 'M' => '#9900CC', # purple 'H' => '#999900', # olive 'S' => '#999900', # olive 'T' => '#999900', # olive 'W' => '#999900', # olive 'P' => '#996600', # brown 'D' => '#3399FF', # skyblue 'N' => '#3399FF', # skyblue 'Y' => '#3399FF', # skyblue 'E' => '#0000FF', # blue 'Q' => '#0000FF', # blue 'R' => '#990000', 'K' => '#999999', # gray }, 'standard_area' => { 'G' => '#FF66FF', # pink 'A' => '#FF3300', # red 'S' => '#FF3300', # red 'C' => '#9900CC', # purple 'P' => '#9900CC', # purple 'D' => '#999900', # olive 'N' => '#999900', # olive 'T' => '#999900', # olive 'V' => '#999900', # olive 'E' => '#996600', # brown 'I' => '#996600', # brown 'H' => '#3399FF', # skyblue 'L' => '#3399FF', # skyblue 'M' => '#3399FF', # skyblue 'Q' => '#3399FF', # skyblue 'F' => '#0000FF', # blue 'K' => '#0000FF', # blue 'Y' => '#990000', 'R' => '#999999', # gray 'W' => '#999999', # gray }, 'hydropathy' => 

       {

'D' => '#FF0000', 'E' => '#FF0000', 'H' => '#0000FF', 'K' => '#0000FF', 'R' => '#0000FF', 'C' => '#FF9900', 'G' => '#FF9900', 'N' => '#FF9900', 'Q' => '#FF9900', 'S' => '#FF9900', 'T' => '#FF9900', 'Y' => '#FF9900', 'A' => '#339900', 'F' => '#339900', 'I' => '#339900', 'L' => '#339900', 'M' => '#339900', 'P' => '#339900', 'V' => '#339900', 'W' => '#339900', }, 'charge' => 

       {

'D' => '#FF0000', 'E' => '#FF0000', 'H' => '#0000FF', 'K' => '#0000FF', 'R' => '#0000FF', }, 

       'chemical'      =>
       {

'D' => '#FF0000', # 'E' => '#FF0000', # 'H' => '#0000FF', # 'K' => '#0000FF', # 'R' => '#0000FF', # 'A' => '#9900CC', # purple 'G' => '#9900CC', # purple 'I' => '#9900CC', # purple 'L' => '#9900CC', # purple 'V' => '#9900CC', # purple 'N' => '#999900', # olive 'Q' => '#999900', # olive 'F' => '#996600', # brown 'W' => '#996600', # brown 'Y' => '#996600', # brown 'S' => '#3399FF', # skyblue 'T' => '#3399FF', # skyblue 'P' => '#990000', 'C' => '#999999', # gray 'M' => '#999999', # gray }, 'structure' => { 'D' => '#FF9900', 'E' => '#FF9900', 'H' => '#FF9900', 'K' => '#FF9900', 'N' => '#FF9900', 'Q' => '#FF9900', 'R' => '#FF9900', 'F' => '#339900', 'I' => '#339900', 'L' => '#339900', 'M' => '#339900', 'V' => '#339900', 'A' => '#3399FF', # skyblue 'C' => '#3399FF', # skyblue 'G' => '#3399FF', # skyblue 'P' => '#3399FF', # skyblue 'S' => '#3399FF', # skyblue 'T' => '#3399FF', # skyblue 'W' => '#3399FF', # skyblue 'Y' => '#3399FF', # skyblue }, 

   };                           
if($params->{blocks})
   {

${$params->{motif}} =~s/(\w{$params->{blocks}})/$1 /g; 

   }

${$params->{'motif'}} =~ s/([@{[join "",keys %{$residue_color_schemes ->{$params->{schema}}}]}])/{$params->{schema}}->{$1}\" class="est">$1<\/font>/g; }


  1. ------------------------- Other useful lookup tables -------------------------- #
  2. Source: http://examples.oreilly.com/begperlbio/


   my %three2one = (
     'ALA' => 'A',
     'VAL' => 'V',
     'LEU' => 'L',
     'ILE' => 'I',
     'PRO' => 'P',
     'TRP' => 'W',
     'PHE' => 'F',
     'MET' => 'M',
     'GLY' => 'G',
     'SER' => 'S',
     'THR' => 'T',
     'TYR' => 'Y',
     'CYS' => 'C',
     'ASN' => 'N',
     'GLN' => 'Q',
     'LYS' => 'K',
     'ARG' => 'R',
     'HIS' => 'H',
     'ASP' => 'D',
     'GLU' => 'E',
   );

my(%genetic_code) = (
   
   'TCA' => 'S',    # Serine
   'TCC' => 'S',    # Serine
   'TCG' => 'S',    # Serine
   'TCT' => 'S',    # Serine
   'TTC' => 'F',    # Phenylalanine
   'TTT' => 'F',    # Phenylalanine
   'TTA' => 'L',    # Leucine
   'TTG' => 'L',    # Leucine
   'TAC' => 'Y',    # Tyrosine
   'TAT' => 'Y',    # Tyrosine
   'TAA' => '_',    # Stop
   'TAG' => '_',    # Stop
   'TGC' => 'C',    # Cysteine
   'TGT' => 'C',    # Cysteine
   'TGA' => '_',    # Stop
   'TGG' => 'W',    # Tryptophan
   'CTA' => 'L',    # Leucine
   'CTC' => 'L',    # Leucine
   'CTG' => 'L',    # Leucine
   'CTT' => 'L',    # Leucine
   'CCA' => 'P',    # Proline
   'CCC' => 'P',    # Proline
   'CCG' => 'P',    # Proline
   'CCT' => 'P',    # Proline
   'CAC' => 'H',    # Histidine
   'CAT' => 'H',    # Histidine
   'CAA' => 'Q',    # Glutamine
   'CAG' => 'Q',    # Glutamine
   'CGA' => 'R',    # Arginine
   'CGC' => 'R',    # Arginine
   'CGG' => 'R',    # Arginine
   'CGT' => 'R',    # Arginine
   'ATA' => 'I',    # Isoleucine
   'ATC' => 'I',    # Isoleucine
   'ATT' => 'I',    # Isoleucine
   'ATG' => 'M',    # Methionine
   'ACA' => 'T',    # Threonine
   'ACC' => 'T',    # Threonine
   'ACG' => 'T',    # Threonine
   'ACT' => 'T',    # Threonine
   'AAC' => 'N',    # Asparagine
   'AAT' => 'N',    # Asparagine
   'AAA' => 'K',    # Lysine
   'AAG' => 'K',    # Lysine
   'AGC' => 'S',    # Serine
   'AGT' => 'S',    # Serine
   'AGA' => 'R',    # Arginine
   'AGG' => 'R',    # Arginine
   'GTA' => 'V',    # Valine
   'GTC' => 'V',    # Valine
   'GTG' => 'V',    # Valine
   'GTT' => 'V',    # Valine
   'GCA' => 'A',    # Alanine
   'GCC' => 'A',    # Alanine
   'GCG' => 'A',    # Alanine
   'GCT' => 'A',    # Alanine
   'GAC' => 'D',    # Aspartic Acid
   'GAT' => 'D',    # Aspartic Acid
   'GAA' => 'E',    # Glutamic Acid
   'GAG' => 'E',    # Glutamic Acid
   'GGA' => 'G',    # Glycine
   'GGC' => 'G',    # Glycine
   'GGG' => 'G',    # Glycine
   'GGT' => 'G',    # Glycine
   );

my %iub2character_class = (
   
       A => 'A',
       C => 'C',
       G => 'G',
       T => 'T',
       R => '[GA]',
       Y => '[CT]',
       M => '[AC]',
       K => '[GT]',
       S => '[GC]',
       W => '[AT]',
       B => '[CGT]',
       D => '[AGT]',
       H => '[ACT]',
       V => '[ACG]',
       N => '[ACGT]',
   );
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