synonymy.pl

#!/usr/bin/env perl
## Pombert Lab, 2017-2018 Illinois Tech

my $version = '0.5c';
my $name = 'synonymy.pl';
my $updated = '2024-05-28';

use strict;
use warnings;
use Getopt::Long qw(GetOptions);
use File::Basename;
use File::Path qw(make_path);

#########################################################################
### Command line options
#########################################################################

my $usage = <<"OPTIONS";
NAME        ${name}
VERSION     ${version}
UPDATED     ${updated}
SYNOPSIS    Sort SNPs per type (CDS, tRNA, rRNA or intergenic) and synonymous or non-synonymous, if applicable
NOTE        Does not work with introns yet
        
USAGE      ${name} \\
             -gcode 1 \\
             -fa reference.fasta \\
             -ref reference.gbk \\
             -format gb \\
             -vcf *.vcf \\
             -o SYNONYMY \\
             -p synonymy

OPTIONS:
-fa (--fasta)    Reference genome in fasta format
-r (--ref)       Reference genome annotation in GBK or GFF format
-f (--format)    Reference file format; gb or gff [default: gff]
-vcf (--vcf)     SNPs in Variant Calling Format (VCF)
-o (--outdir)    Output directory [Default: ./]
-p (--prefix)    Table prefix [Default: synonymy]
-gc (--gcode)    NCBI genetic code [Default: 1]
                   1  - The Standard Code
                   2  - The Vertebrate Mitochondrial Code
                   3  - The Yeast Mitochondrial Code
                   4  - The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
                   11 - The Bacterial, Archaeal and Plant Plastid Code
                   # For complete list, see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
-v (--verbose)   Adds verbosity
--version        Show script version
OPTIONS

unless (@ARGV){
    print "\n$usage\n";
    exit(0);
};

## GetOptions
my $fasta;
my $ref;
my $format = 'gff';
my @vcf;
my $outdir = './';
my $prefix = 'synonymy';
my $gc = '1';
my $verbose;
my $sc_version;
GetOptions(
    'fa|fasta=s' => \$fasta,
    'r|ref=s' => \$ref,
    'f|format=s' => \$format,
    'vcf=s@{1,}' => \@vcf,
    'o|outdir=s' => \$outdir,
    'p|prefix=s' => \$prefix,
    'gc|gcode=i' => \$gc,
    'v|verbose' => \$verbose,
	'version' => \$sc_version
);

#########################################################################
### Version
#########################################################################

if ($sc_version){
    print "\n";
    print "Script:     $name\n";
    print "Version:    $version\n";
    print "Updated:    $updated\n\n";
    exit(0);
}

#########################################################################
### Output directory
#########################################################################

unless (-d $outdir){
	make_path( $outdir, { mode => 0755 } ) or die "Can't create folder $outdir: $!\n";
}

#########################################################################
### Building database of sequences
#########################################################################

open FASTA, '<', $fasta or die "Can't read FASTA file $fasta: $!\n";
my %sequences;
my $contig;

while (my $line = <FASTA>){
    chomp $line;
    if ($line =~ /^>(\S+)/){
		$contig = $1;
	}
    else{
		$sequences{$contig} .= $line;
	}
}

#########################################################################
### Building database of features
#########################################################################

open REF, '<', $ref or die "Can't read reference file $ref: $!\n";

my %features; 
my %loci; ## loci -> contig -> genomic_locus (e.g. 79553) = corresponding feature
my $type;
my $start;
my $end;
my $strand;
my $gene_id;
my $locus_tag;
my $parent;
my $product;

if ($format eq 'gff'){

    while (my $line = <REF>){

        chomp $line;

        if ($line =~ /^#/){
			next;
		}
        elsif ($line =~ /^ID=/){
			next;
		}

        my @columns = split ("\t", $line);

        $contig = $columns[0];
        $type = $columns[2];
        $start = $columns[3];
        $end = $columns[4];
        $strand = $columns[6];

        ## Putting descriptions into an hash for easy parsing and access
        my $description = $columns[8];
        my %descriptors;
        my @descriptors = split (";", $description);
        foreach my $desc (@descriptors){
            my ($key, $value) = $desc =~ /(.*?)=(.*)/;
            $descriptors{$key} = $value;
        }

        $gene_id = $descriptors{'ID'};

        if ($type =~ /tRNA|rRNA|CDS/){

            $locus_tag = $descriptors{'locus_tag'};
            $product = $descriptors{'product'};

            ## Populating features DB
            $features{$gene_id}{'type'} = $type;
            $features{$gene_id}{'start'} = $start;
            $features{$gene_id}{'end'} = $end;
            $features{$gene_id}{'strand'} = $strand;
            $features{$gene_id}{'locus_tag'} = $locus_tag;
            $features{$gene_id}{'product'} = $product;

            if ($verbose){
				print "$contig\t$type\t$strand\t$locus_tag\t$product\n";
			}

            ## creating a hash of genomic loci and their associated gene_ID
            for ($start..$end){
                push (@{$loci{$contig}{$_}}, $gene_id);
            }
        }
    }
}

elsif ($format eq 'gb'){
    
    ## Putting the gbk file in a single string, then split per conting
    my $gbk;

	while (my $line = <REF>){
		$gbk .= $line;
	}

    my @contigs = split ("\/\/\n", $gbk);

    ## Parsing contigs
    while (my $cg = shift @contigs){

        my @data = split ("ORIGIN.*?\n", $cg);

        ## $data[0] => annotations
        my ($locus) = $data[0] =~ /LOCUS\s+(\S+)/;
        my ($contig) = $data[0] =~ /VERSION\s+(\S+)/;
        my ($feat) = $data[0] =~ /FEATURES(.*)/s;

        ## $data[1] => sequences
        my $sequence = $data[1];
        $sequence =~ s/[0-9\s\n]//g;

        if ($verbose){
			print "Working on $locus version $contig\n";
		}

        ## Working on features
        my @features = split("     gene            ", $feat);

        while (my $line = shift@features){

            if ($line =~ /\s+(CDS|rRNA|tRNA)\s+.*?(\d+)\.\.(\d+)/m){

                $type = $1;
                $start = $2;
                $end = $3;

                if ($line =~ /complement/){
					$strand = '-';
				}
                else{
					$strand = '+';
				}

                ($locus_tag) = $line =~ /\/locus_tag="(.*?)"/s;
                $locus_tag =~ s/\s{2,}/ /g;
                $locus_tag =~ s/\n//g; ## removing new lines, if any

                ($product) = $line =~ /\/product="(.*?)"/s;
                $product =~ s/\s{2,}/ /g;
                $product =~ s/\n//g; ## removing new lines, if any

                $features{$locus_tag}{'type'} = $type;
                $features{$locus_tag}{'start'} = $start;
                $features{$locus_tag}{'end'} = $end;
                $features{$locus_tag}{'strand'} = $strand;
                $features{$locus_tag}{'locus_tag'} = $locus_tag;
                $features{$locus_tag}{'product'} = $product;

                if ($verbose){
					print "$contig\t$type\t$strand\t$locus_tag\t$product\n";
				}

                ## creating a hash of genomic loci and their associated gene_ID
                for ($start..$end){
                    push (@{$loci{$contig}{$_}}, $locus_tag);
                }
            }
        }
    }
}

#########################################################################
### Populating genetic code from subroutine
#########################################################################

my %gcodes;
gcodes();

#########################################################################
### Working on VCF files
#########################################################################

my $codon;
my $snp;
my $revcodon;
my $revsnp;
my $locus;

while (my $vcf = shift@vcf){
    
    ## Reading VCF file
    open VCF, '<', $vcf or die "Can't read VCF file $vcf: $!\n";
    my $basename = fileparse($vcf);
    $basename =~ s/\.\w+$//;

    ## Creating output tables per VCF
    my $feature_table = "${outdir}/$basename.$prefix.features.tsv";
    my $intergenic_table = "${outdir}/$basename.$prefix.intergenic.tsv";
    open FEAT, '>', $feature_table or die "Can't create $feature_table: $!\n";
    open INTER, '>', $intergenic_table or die "Can't create $intergenic_table: $!\n";

    my @feat_headers = (
        'Locus_tag',
        'Reference Contig',
        'VCF file',
        'Type',
        'Start',
        'End',
        'Strandedness',
        'Product',
        'Variant Position',
        'Reference',
        'Variant',
        'Synonymy',
        'Genetic Code',
        'RefCodon',
        'VarCodon',
        'Frequency',
        'E-value'
    );

    for (0..$#feat_headers-1){
		print FEAT "$feat_headers[$_]\t";
	}
    print FEAT "$feat_headers[-1]\n";

    my @inter_headers = (
        'Reference Contig',
        'VCF file',
        'Type',
        'Variant Position',
        'Reference',
        'Variant',
        'Frequency',
        'E-value'
    );

    for (0..$#inter_headers-1){
		print INTER "$inter_headers[$_]\t";
	}
    print INTER "$inter_headers[-1]\n";

    while (my $line = <VCF>){

        chomp $line;

        if ($line =~ /^#/){
			next;
		}
        else{

            my @vcf = split("\t", $line);
            $contig = $vcf[0];
            my $position = $vcf[1];
            my $ref = $vcf[3];
            my $alt = $vcf[4];
            
            my @params = split(":", $vcf[9]);
            my $freq = $params[6];
            my $evalue = $params[7];

            if (exists $loci{$contig}{$position}){

                for (0..$#{$loci{$contig}{$position}}){

                    $locus = $loci{$contig}{$position}[$_];

                    $type = $features{$locus}{'type'};
                    $start = $features{$locus}{'start'};
                    $end = $features{$locus}{'end'};
                    $strand = $features{$locus}{'strand'};
                    $locus_tag = $features{$locus}{'locus_tag'};
                    $product = $features{$locus}{'product'};

                    print FEAT "$locus_tag\t$contig\t$vcf\t$type\t$start\t$end\t$strand\t$product\t$position\t$ref\t$alt\t";

                    if ($type eq 'tRNA'){
						print FEAT "N\/A\tN\/A\tN\/A\tN\/A\t";
					}
                    elsif ($type eq 'rRNA'){
						print FEAT "N\/A\tN\/A\tN\/A\tN\/A\t";
					}
                    elsif ($type eq 'CDS'){
                        if (($strand  eq '+') || ($strand  eq 'plus')){
                            if (($position - $start) == 0){
                                $codon = substr($sequences{$contig}, $position-1, 3);
                                $snp = $codon; $snp =~ substr($snp, 0, 1, $alt);
                                translation();
                            }
                            elsif (($position - $start) == 1){
                                $codon = substr($sequences{$contig}, $position-2, 3);
                                $snp = $codon; $snp =~ substr($snp, 1, 1, $alt);
                                translation();
                            }
                            elsif (($position - $start) > 1){
                                my $location = $position - $start + 1;
                                if (($location % 3) == 0){ ## Third codon position
                                    $codon = substr($sequences{$contig}, $position-3, 3); ## this is OK
                                    $snp = $codon; $snp =~ substr($snp, 2, 1, $alt);
                                    translation();
                                }
                                elsif (($location % 3) == 1){ ## First codon position
                                    $codon = substr($sequences{$contig}, $position-1, 3);
                                    $snp = $codon; $snp =~ substr($snp, 0, 1, $alt);
                                    translation();
                                }
                                elsif (($location % 3) == 2){ ## Second codon position
                                    $codon = substr($sequences{$contig}, $position-2, 3);
                                    $snp = $codon; $snp =~ substr($snp, 1, 1, $alt);
                                    translation();
                                }
                            }
                        }
                        elsif (($strand  eq '-') || ($strand  eq 'minus')){
                            if (($end - $position) == 0){
                                $revcodon = substr($sequences{$contig}, $position-3, 3);
                                $revsnp = $revcodon; $revsnp =~ substr($revsnp, 2, 1, $alt);
                                rev(); translation();
                            }
                            elsif (($end - $position) == 1){
                                $revcodon  = substr($sequences{$contig}, $position-2, 3);
                                $revsnp = $revcodon; $revsnp =~ substr($revsnp, 1, 1, $alt);
                                rev(); translation();
                            }
                            elsif (($end - $position) > 1){
                                my $location = $end - $position + 1;
                                if (($location % 3) == 0){ ## Third codon position
                                    $revcodon = substr($sequences{$contig}, $position-1, 3);
                                    $revsnp = $revcodon; $revsnp =~ substr($revsnp, 0, 1, $alt);
                                    rev(); translation();
                                }
                                elsif (($location % 3) == 1){ ## First codon position
                                    $revcodon = substr($sequences{$contig}, $position-3, 3);
                                    $revsnp = $revcodon; $revsnp =~ substr($revsnp, 2, 1, $alt);
                                    rev(); translation();
                                }
                                elsif (($location % 3) == 2){ ## Second codon position
                                    $revcodon = substr($sequences{$contig}, $position-2, 3);
                                    $revsnp = $revcodon; $revsnp =~ substr($revsnp, 1, 1, $alt);
                                    rev(); translation();
                                }
                            }
                        }
                    }
                    print FEAT "$freq\t$evalue\n";
                }
            }
            else {
				print INTER "$contig\t$vcf\tintergenic\t$position\t$ref\t$alt\t$freq\t$evalue\n"
			}
        }
    }
}

## Subroutines
sub rev{
    $codon = reverse($revcodon); $codon =~ tr/ATGCNatgcn/TACGNtacgn/;
    $snp = reverse($revsnp); $snp =~ tr/ATGCNatgcn/TACGNtacgn/;
}

sub translation{
    $codon = uc($codon); $snp = uc($snp);
    if ($codon =~ /[^ATGCatgc]/){print FEAT "ambiguous bases\t$gc\t$codon\t$snp\t";}
    elsif ($gcodes{$gc}{$codon} eq $gcodes{$gc}{$snp}){print FEAT "synonym\t$gc\t$codon\t$snp\t";}
    elsif ($gcodes{$gc}{$codon} ne $gcodes{$gc}{$snp}){print FEAT "non-syn\t$gc\t$codon\t$snp\t";}
}

sub gcodes{ ## NCBI Genetic codes
    %gcodes = (
        1 => { ## The Standard Code (transl_table=1)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',   
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        2 => { ## The Vertebrate Mitochondrial Code (transl_table=2)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'M', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => '*',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => '*',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        3 => { ## The Yeast Mitochondrial Code (transl_table=3)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'T', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'T', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'T', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'T', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'M', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        4 => { ## The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code (transl_table=4)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',  
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',  
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',  
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',  
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',  
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G' 
        },
        5 => { ## The Invertebrate Mitochondrial Code (transl_table=5)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',  
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',  
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
            'ATA' => 'M', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'S',  
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'S',  
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',  
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'  
        },
        6 => { ## The Ciliate, Dasycladacean and Hexamita Nuclear Code (transl_table=6)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C', 
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C', 
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'Q', 'TGA' => '*', 
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'Q', 'TGG' => 'W', 
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R', 
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R', 
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R', 
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R', 
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S', 
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S', 
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R', 
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R', 
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G', 
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G', 
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G', 
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G' 
        },
        9 => { ## The Echinoderm and Flatworm Mitochondrial Code (transl_table=9)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',  
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',  
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'N', 'AGA' => 'S',  
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'S',  
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'  
        },
        10 => { ## The Euplotid Nuclear Code (transl_table=10)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'C',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        11 => { ## The Bacterial, Archaeal and Plant Plastid Code (transl_table=11)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',  
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',  
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',  
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',  
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',  
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'  
        },
        12 => { ## The Alternative Yeast Nuclear Code (transl_table=12)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'S', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        13 => { ## The Ascidian Mitochondrial Code (transl_table=13)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'M', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'G',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'G',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G',
        },
        14 => { ## The Alternative Flatworm Mitochondrial Code (transl_table=14)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'Y', 'TGA' => 'W',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'N', 'AGA' => 'S',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'S',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G',
        },
        16 => { ## Chlorophycean Mitochondrial Code (transl_table=16)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'L', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        21 => { ## Trematode Mitochondrial Code (transl_table=21)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',  
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',  
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
            'ATA' => 'M', 'ACA' => 'T', 'AAA' => 'N', 'AGA' => 'S',  
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'S',  
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',  
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'  
        },
        22 => { ## Scenedesmus obliquus Mitochondrial Code (transl_table=22)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
            'TTA' => 'L', 'TCA' => '*', 'TAA' => '*', 'TGA' => '*',  
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'L', 'TGG' => 'W',  
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',  
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',  
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',  
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'  
        },
        23 => { ## Thraustochytrium Mitochondrial Code (transl_table=23)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => '*', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        24 => { ## Pterobranchia Mitochondrial Code (transl_table=24)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'S',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'K',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        25 => { ## Candidate Division SR1 and Gracilibacteria Code (transl_table=25)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'G',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        26 => { ## Pachysolen tannophilus Nuclear Code (transl_table=26)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'A', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        27 => { ## Karyorelict Nuclear (transl_table=27)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'Q', 'TGA' => 'W',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'Q', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        28 => { ## Condylostoma Nuclear (transl_table=28)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'Q', 'TGA' => 'W',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'Q', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        29 => { ## Mesodinium Nuclear (transl_table=29)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'Y', 'TGA' => '*',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'Y', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        30 => { ## Peritrich Nuclear (transl_table=30)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'E', 'TGA' => '*',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'E', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
        31 => { ## Blastocrithidia Nuclear (transl_table=31)
            'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
            'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
            'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'E', 'TGA' => 'W',
            'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'E', 'TGG' => 'W',
            'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
            'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
            'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
            'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
            'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
            'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
            'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
            'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
            'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
            'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
            'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
            'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
        },
    );
}