# Copyright 2000 Andrew Dalke. All rights reserved. # # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". # Please see the LICENSE file that should have been included as part of this # package. """Codon tables based on those from the NCBI. These tables are based on parsing the NCBI file ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt using Scripts/update_ncbi_codon_table.py Last updated at Version 4.4 (May 2019) """ from typing import Optional from Bio.Data import IUPACData unambiguous_dna_by_name = {} unambiguous_dna_by_id = {} unambiguous_rna_by_name = {} unambiguous_rna_by_id = {} generic_by_name = {} # unambiguous DNA or RNA generic_by_id = {} # unambiguous DNA or RNA ambiguous_dna_by_name = {} ambiguous_dna_by_id = {} ambiguous_rna_by_name = {} ambiguous_rna_by_id = {} ambiguous_generic_by_name = {} # ambiguous DNA or RNA ambiguous_generic_by_id = {} # ambiguous DNA or RNA # standard IUPAC unambiguous codons standard_dna_table = None standard_rna_table = None # In the future, the back_table could return a statistically # appropriate distribution of codons, so do not cache the results of # back_table lookups! class TranslationError(Exception): """Container for translation specific exceptions.""" class CodonTable: """A codon-table, or genetic code.""" forward_table: dict[str, str] = {} # only includes codons which actually code back_table: dict[str, str] = {} # for back translations start_codons: list[str] = [] stop_codons: list[str] = [] # Not always called from derived classes! def __init__( self, nucleotide_alphabet: Optional[str] = None, protein_alphabet: Optional[str] = None, forward_table: dict[str, str] = forward_table, back_table: dict[str, str] = back_table, start_codons: list[str] = start_codons, stop_codons: list[str] = stop_codons, ) -> None: """Initialize the class.""" self.nucleotide_alphabet = nucleotide_alphabet self.protein_alphabet = protein_alphabet self.forward_table = forward_table self.back_table = back_table self.start_codons = start_codons self.stop_codons = stop_codons def __str__(self): """Return a simple text representation of the codon table. e.g.:: >>> import Bio.Data.CodonTable >>> print(Bio.Data.CodonTable.standard_dna_table) Table 1 Standard, SGC0 | T | C | A | G | --+---------+---------+---------+---------+-- T | TTT F | TCT S | TAT Y | TGT C | T T | TTC F | TCC S | TAC Y | TGC C | C ... G | GTA V | GCA A | GAA E | GGA G | A G | GTG V | GCG A | GAG E | GGG G | G --+---------+---------+---------+---------+-- >>> print(Bio.Data.CodonTable.generic_by_id[1]) Table 1 Standard, SGC0 | U | C | A | G | --+---------+---------+---------+---------+-- U | UUU F | UCU S | UAU Y | UGU C | U U | UUC F | UCC S | UAC Y | UGC C | C ... G | GUA V | GCA A | GAA E | GGA G | A G | GUG V | GCG A | GAG E | GGG G | G --+---------+---------+---------+---------+-- """ if self.id: answer = "Table %i" % self.id else: answer = "Table ID unknown" if self.names: answer += " " + ", ".join([x for x in self.names if x]) # Use the main four letters (and the conventional ordering) # even for ambiguous tables letters = self.nucleotide_alphabet if letters is not None and "T" in letters: letters = "TCAG" else: # Should be either RNA or generic nucleotides, # e.g. Bio.Data.CodonTable.generic_by_id[1] letters = "UCAG" # Build the table... answer += "\n\n" answer += " |" + "|".join(f" {c2} " for c2 in letters) + "|" answer += "\n--+" + "+".join("---------" for c2 in letters) + "+--" for c1 in letters: for c3 in letters: line = c1 + " |" for c2 in letters: codon = c1 + c2 + c3 line += f" {codon}" if codon in self.stop_codons: line += " Stop|" else: try: amino = self.forward_table[codon] except KeyError: amino = "?" except TranslationError: amino = "?" if codon in self.start_codons: line += f" {amino}(s)|" else: line += f" {amino} |" line += " " + c3 answer += "\n" + line answer += "\n--+" + "+".join("---------" for c2 in letters) + "+--" return answer def make_back_table(table, default_stop_codon): """Back a back-table (naive single codon mapping). ONLY RETURNS A SINGLE CODON, chosen from the possible alternatives based on their sort order. """ # Do the sort so changes in the hash implementation won't affect # the result when one amino acid is coded by more than one codon. back_table = {} for key in sorted(table): back_table[table[key]] = key back_table[None] = default_stop_codon return back_table class NCBICodonTable(CodonTable): """Codon table for generic nucleotide sequences.""" nucleotide_alphabet: Optional[str] = None protein_alphabet = IUPACData.protein_letters def __init__(self, id, names, table, start_codons, stop_codons): """Initialize the class.""" self.id = id self.names = names self.forward_table = table self.back_table = make_back_table(table, stop_codons[0]) self.start_codons = start_codons self.stop_codons = stop_codons def __repr__(self): """Represent the NCBI codon table class as a string for debugging.""" return f"{self.__class__.__name__}(id={self.id!r}, names={self.names!r}, ...)" class NCBICodonTableDNA(NCBICodonTable): """Codon table for unambiguous DNA sequences.""" nucleotide_alphabet = IUPACData.unambiguous_dna_letters class NCBICodonTableRNA(NCBICodonTable): """Codon table for unambiguous RNA sequences.""" nucleotide_alphabet = IUPACData.unambiguous_rna_letters # ######## Deal with ambiguous forward translations class AmbiguousCodonTable(CodonTable): """Base codon table for ambiguous sequences.""" def __init__( self, codon_table, ambiguous_nucleotide_alphabet, ambiguous_nucleotide_values, ambiguous_protein_alphabet, ambiguous_protein_values, ): """Initialize the class.""" CodonTable.__init__( self, ambiguous_nucleotide_alphabet, ambiguous_protein_alphabet, AmbiguousForwardTable( codon_table.forward_table, ambiguous_nucleotide_values, ambiguous_protein_values, ), codon_table.back_table, # These two are WRONG! I need to get the # list of ambiguous codons which code for # the stop codons XXX list_ambiguous_codons( codon_table.start_codons, ambiguous_nucleotide_values ), list_ambiguous_codons(codon_table.stop_codons, ambiguous_nucleotide_values), ) self._codon_table = codon_table # Be sneaky and forward attribute lookups to the original table. # This lets us get the names, if the original table is an NCBI # table. def __getattr__(self, name): """Forward attribute lookups to the original table.""" return getattr(self._codon_table, name) def list_possible_proteins(codon, forward_table, ambiguous_nucleotide_values): """Return all possible encoded amino acids for ambiguous codon.""" c1, c2, c3 = codon x1 = ambiguous_nucleotide_values[c1] x2 = ambiguous_nucleotide_values[c2] x3 = ambiguous_nucleotide_values[c3] possible = {} stops = [] for y1 in x1: for y2 in x2: for y3 in x3: try: possible[forward_table[y1 + y2 + y3]] = 1 except KeyError: # If tripping over a stop codon stops.append(y1 + y2 + y3) if stops: if possible: raise TranslationError( f"ambiguous codon {codon!r} codes for both proteins and stop codons" ) # This is a true stop codon - tell the caller about it raise KeyError(codon) return list(possible) def list_ambiguous_codons(codons, ambiguous_nucleotide_values): """Extend a codon list to include all possible ambiguous codons. e.g.:: ['TAG', 'TAA'] -> ['TAG', 'TAA', 'TAR'] ['UAG', 'UGA'] -> ['UAG', 'UGA', 'URA'] Note that ['TAG', 'TGA'] -> ['TAG', 'TGA'], this does not add 'TRR' (which could also mean 'TAA' or 'TGG'). Thus only two more codons are added in the following: e.g.:: ['TGA', 'TAA', 'TAG'] -> ['TGA', 'TAA', 'TAG', 'TRA', 'TAR'] Returns a new (longer) list of codon strings. """ # Note ambiguous_nucleotide_values['R'] = 'AG' (etc) # This will generate things like 'TRR' from ['TAG', 'TGA'], which # we don't want to include: c1_list = sorted( letter for letter, meanings in ambiguous_nucleotide_values.items() if {codon[0] for codon in codons}.issuperset(set(meanings)) ) c2_list = sorted( letter for letter, meanings in ambiguous_nucleotide_values.items() if {codon[1] for codon in codons}.issuperset(set(meanings)) ) c3_list = sorted( letter for letter, meanings in ambiguous_nucleotide_values.items() if {codon[2] for codon in codons}.issuperset(set(meanings)) ) # candidates is a list (not a set) to preserve the iteration order candidates = [] for c1 in c1_list: for c2 in c2_list: for c3 in c3_list: codon = c1 + c2 + c3 if codon not in candidates and codon not in codons: candidates.append(codon) answer = codons[:] # copy # print("Have %i new candidates" % len(candidates)) for ambig_codon in candidates: wanted = True # e.g. 'TRR' -> 'TAA', 'TAG', 'TGA', 'TGG' for codon in [ c1 + c2 + c3 for c1 in ambiguous_nucleotide_values[ambig_codon[0]] for c2 in ambiguous_nucleotide_values[ambig_codon[1]] for c3 in ambiguous_nucleotide_values[ambig_codon[2]] ]: if codon not in codons: # This ambiguous codon can code for a non-stop, exclude it! wanted = False # print("Rejecting %s" % ambig_codon) continue if wanted: answer.append(ambig_codon) return answer assert list_ambiguous_codons(["TGA", "TAA"], IUPACData.ambiguous_dna_values) == [ "TGA", "TAA", "TRA", ] assert list_ambiguous_codons(["TAG", "TGA"], IUPACData.ambiguous_dna_values) == [ "TAG", "TGA", ] assert list_ambiguous_codons(["TAG", "TAA"], IUPACData.ambiguous_dna_values) == [ "TAG", "TAA", "TAR", ] assert list_ambiguous_codons(["UAG", "UAA"], IUPACData.ambiguous_rna_values) == [ "UAG", "UAA", "UAR", ] assert list_ambiguous_codons(["TGA", "TAA", "TAG"], IUPACData.ambiguous_dna_values) == [ "TGA", "TAA", "TAG", "TAR", "TRA", ] # Forward translation is "onto", that is, any given codon always maps # to the same protein, or it doesn't map at all. Thus, I can build # off of an existing table to produce the ambiguous mappings. # # This handles the general case. Perhaps it's overkill? # >>> t = CodonTable.ambiguous_dna_by_id[1] # >>> t.forward_table["AAT"] # 'N' # >>> t.forward_table["GAT"] # 'D' # >>> t.forward_table["RAT"] # 'B' # >>> t.forward_table["YTA"] # 'L' class AmbiguousForwardTable: """Forward table for translation of ambiguous nucleotide sequences.""" def __init__(self, forward_table, ambiguous_nucleotide, ambiguous_protein): """Initialize the class.""" self.forward_table = forward_table self.ambiguous_nucleotide = ambiguous_nucleotide self.ambiguous_protein = ambiguous_protein inverted = {} for name, val in ambiguous_protein.items(): for c in val: x = inverted.get(c, {}) x[name] = 1 inverted[c] = x for name, val in inverted.items(): inverted[name] = list(val) self._inverted = inverted self._cache = {} def __contains__(self, codon): """Check if codon works as key for ambiguous forward_table. Only returns 'True' if forward_table[codon] returns a value. """ try: self.__getitem__(codon) return True except (KeyError, TranslationError): return False def get(self, codon, failobj=None): """Implement get for dictionary-like behaviour.""" try: return self.__getitem__(codon) except KeyError: return failobj def __getitem__(self, codon): """Implement dictionary-like behaviour for AmbiguousForwardTable. forward_table[codon] will either return an amino acid letter, or throws a KeyError (if codon does not encode an amino acid) or a TranslationError (if codon does encode for an amino acid, but either is also a stop codon or does encode several amino acids, for which no unique letter is available in the given alphabet. """ try: x = self._cache[codon] except KeyError: pass else: if x is TranslationError: raise TranslationError(codon) # no unique translation if x is KeyError: raise KeyError(codon) # it's a stop codon return x try: x = self.forward_table[codon] self._cache[codon] = x return x except KeyError: pass # XXX Need to make part of this into a method which returns # a list of all possible encodings for a codon! try: possible = list_possible_proteins( codon, self.forward_table, self.ambiguous_nucleotide ) except KeyError: self._cache[codon] = KeyError raise KeyError(codon) from None # stop codon except TranslationError: self._cache[codon] = TranslationError raise TranslationError(codon) # does not code assert len(possible) > 0, "unambiguous codons must code" # Hah! Only one possible protein, so use it if len(possible) == 1: self._cache[codon] = possible[0] return possible[0] # See if there's an ambiguous protein encoding for the multiples. # Find residues which exist in every coding set. ambiguous_possible = {} for amino in possible: for term in self._inverted[amino]: ambiguous_possible[term] = ambiguous_possible.get(term, 0) + 1 n = len(possible) possible = [] for amino, val in ambiguous_possible.items(): if val == n: possible.append(amino) # No amino acid encoding for the results if len(possible) == 0: self._cache[codon] = TranslationError raise TranslationError(codon) # no valid translation # All of these are valid, so choose one # To be unique, sort by smallet ambiguity then alphabetically # Can get this if "X" encodes for everything. # def _sort(x, y, table = self.ambiguous_protein): # a = cmp(len(table[x]), len(table[y])) # if a == 0: # return cmp(x, y) # return a # Sort by key is 2.x and 3.x compatible possible.sort(key=lambda x: (len(self.ambiguous_protein[x]), x)) x = possible[0] self._cache[codon] = x return x def register_ncbi_table(name, alt_name, id, table, start_codons, stop_codons): """Turn codon table data into objects (PRIVATE). The data is stored in the dictionaries. """ # In most cases names are divided by "; ", however there is also # Table 11 'Bacterial, Archaeal and Plant Plastid Code', previously # 'Bacterial and Plant Plastid' which used to be just 'Bacterial' names = [ x.strip() for x in name.replace(" and ", "; ").replace(", ", "; ").split("; ") ] dna = NCBICodonTableDNA(id, names + [alt_name], table, start_codons, stop_codons) ambig_dna = AmbiguousCodonTable( dna, IUPACData.ambiguous_dna_letters, IUPACData.ambiguous_dna_values, IUPACData.extended_protein_letters, IUPACData.extended_protein_values, ) # replace all T's with U's for the RNA tables rna_table = {} generic_table = {} for codon, val in table.items(): generic_table[codon] = val codon = codon.replace("T", "U") generic_table[codon] = val rna_table[codon] = val rna_start_codons = [] generic_start_codons = [] for codon in start_codons: generic_start_codons.append(codon) # We need to check if 'T' is in the codon, otherwise # generic_start_codons may contain duplicates if "T" in codon: codon = codon.replace("T", "U") generic_start_codons.append(codon) rna_start_codons.append(codon) rna_stop_codons = [] generic_stop_codons = [] for codon in stop_codons: generic_stop_codons.append(codon) if "T" in codon: codon = codon.replace("T", "U") generic_stop_codons.append(codon) rna_stop_codons.append(codon) generic = NCBICodonTable( id, names + [alt_name], generic_table, generic_start_codons, generic_stop_codons ) # The following isn't very elegant, but seems to work nicely. _merged_values = dict(IUPACData.ambiguous_rna_values.items()) _merged_values["T"] = "U" ambig_generic = AmbiguousCodonTable( generic, None, _merged_values, IUPACData.extended_protein_letters, IUPACData.extended_protein_values, ) rna = NCBICodonTableRNA( id, names + [alt_name], rna_table, rna_start_codons, rna_stop_codons ) ambig_rna = AmbiguousCodonTable( rna, IUPACData.ambiguous_rna_letters, IUPACData.ambiguous_rna_values, IUPACData.extended_protein_letters, IUPACData.extended_protein_values, ) if id == 1: global standard_dna_table, standard_rna_table standard_dna_table = dna standard_rna_table = rna unambiguous_dna_by_id[id] = dna unambiguous_rna_by_id[id] = rna generic_by_id[id] = generic ambiguous_dna_by_id[id] = ambig_dna ambiguous_rna_by_id[id] = ambig_rna ambiguous_generic_by_id[id] = ambig_generic if alt_name is not None: names.append(alt_name) for name in names: unambiguous_dna_by_name[name] = dna unambiguous_rna_by_name[name] = rna generic_by_name[name] = generic ambiguous_dna_by_name[name] = ambig_dna ambiguous_rna_by_name[name] = ambig_rna ambiguous_generic_by_name[name] = ambig_generic # The rest of this file is automatically generated, here we turn off # black formatting in order to keep the codon tables compact. # # fmt: off ########################################################################## # Start of auto-generated output from Scripts/update_ncbi_codon_table.py # ########################################################################## # Data from NCBI genetic code table version 4.5 register_ncbi_table( name="Standard", alt_name="SGC0", id=1, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG", "TGA"], start_codons=["TTG", "CTG", "ATG"], ) register_ncbi_table( name="Vertebrate Mitochondrial", alt_name="SGC1", id=2, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "M", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", # noqa: E241 "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG", "AGA", "AGG"], start_codons=["ATT", "ATC", "ATA", "ATG", "GTG"], ) register_ncbi_table( name="Yeast Mitochondrial", alt_name="SGC2", id=3, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "T", "CTC": "T", "CTA": "T", "CTG": "T", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "M", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG"], start_codons=["ATA", "ATG", "GTG"], ) register_ncbi_table( name="Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate " "Mitochondrial; Mycoplasma; Spiroplasma", alt_name="SGC3", id=4, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG"], start_codons=["TTA", "TTG", "CTG", "ATT", "ATC", "ATA", "ATG", "GTG"], ) register_ncbi_table( name="Invertebrate Mitochondrial", alt_name="SGC4", id=5, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "M", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "S", "AGG": "S", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG"], start_codons=["TTG", "ATT", "ATC", "ATA", "ATG", "GTG"], ) register_ncbi_table( name="Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear", alt_name="SGC5", id=6, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAA": "Q", "TAG": "Q", "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TGA"], start_codons=["ATG"], ) register_ncbi_table( name="Echinoderm Mitochondrial; Flatworm Mitochondrial", alt_name="SGC8", id=9, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "N", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "S", "AGG": "S", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG"], start_codons=["ATG", "GTG"], ) register_ncbi_table( name="Euplotid Nuclear", alt_name="SGC9", id=10, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "C", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG"], start_codons=["ATG"], ) register_ncbi_table( name="Bacterial, Archaeal and Plant Plastid", alt_name=None, id=11, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG", "TGA"], start_codons=["TTG", "CTG", "ATT", "ATC", "ATA", "ATG", "GTG"], ) register_ncbi_table( name="Alternative Yeast Nuclear", alt_name=None, id=12, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "S", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG", "TGA"], start_codons=["CTG", "ATG"], ) register_ncbi_table( name="Ascidian Mitochondrial", alt_name=None, id=13, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "M", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "G", "AGG": "G", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG"], start_codons=["TTG", "ATA", "ATG", "GTG"], ) register_ncbi_table( name="Alternative Flatworm Mitochondrial", alt_name=None, id=14, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAA": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "N", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "S", "AGG": "S", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAG"], start_codons=["ATG"], ) register_ncbi_table( name="Blepharisma Macronuclear", alt_name=None, id=15, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAG": "Q", # noqa: E241 "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TGA"], start_codons=["ATG"], ) register_ncbi_table( name="Chlorophycean Mitochondrial", alt_name=None, id=16, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAG": "L", # noqa: E241 "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TGA"], start_codons=["ATG"], ) register_ncbi_table( name="Trematode Mitochondrial", alt_name=None, id=21, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "M", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "N", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "S", "AGG": "S", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG"], start_codons=["ATG", "GTG"], ) register_ncbi_table( name="Scenedesmus obliquus Mitochondrial", alt_name=None, id=22, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCG": "S", # noqa: E241 "TAT": "Y", "TAC": "Y", "TAG": "L", # noqa: E241 "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TCA", "TAA", "TGA"], start_codons=["ATG"], ) register_ncbi_table( name="Thraustochytrium Mitochondrial", alt_name=None, id=23, table={ "TTT": "F", "TTC": "F", "TTG": "L", # noqa: E241 "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TTA", "TAA", "TAG", "TGA"], start_codons=["ATT", "ATG", "GTG"], ) register_ncbi_table( name="Pterobranchia Mitochondrial", alt_name=None, id=24, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "S", "AGG": "K", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG"], start_codons=["TTG", "CTG", "ATG", "GTG"], ) register_ncbi_table( name="Candidate Division SR1 and Gracilibacteria", alt_name=None, id=25, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "G", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG"], start_codons=["TTG", "ATG", "GTG"], ) register_ncbi_table( name="Pachysolen tannophilus Nuclear", alt_name=None, id=26, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "A", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG", "TGA"], start_codons=["CTG", "ATG"], ) register_ncbi_table( name="Karyorelict Nuclear", alt_name=None, id=27, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAA": "Q", "TAG": "Q", "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TGA"], start_codons=["ATG"], ) register_ncbi_table( name="Condylostoma Nuclear", alt_name=None, id=28, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAA": "Q", "TAG": "Q", "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG", "TGA"], start_codons=["ATG"], ) register_ncbi_table( name="Mesodinium Nuclear", alt_name=None, id=29, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAA": "Y", "TAG": "Y", "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TGA"], start_codons=["ATG"], ) register_ncbi_table( name="Peritrich Nuclear", alt_name=None, id=30, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAA": "E", "TAG": "E", "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TGA"], start_codons=["ATG"], ) register_ncbi_table( name="Blastocrithidia Nuclear", alt_name=None, id=31, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAA": "E", "TAG": "E", "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TAG"], start_codons=["ATG"], ) register_ncbi_table( name="Balanophoraceae Plastid", alt_name=None, id=32, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAG": "W", # noqa: E241 "TGT": "C", "TGC": "C", "TGG": "W", # noqa: E241 "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R", "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAA", "TGA"], start_codons=["TTG", "CTG", "ATT", "ATC", "ATA", "ATG", "GTG"], ) register_ncbi_table( name="Cephalodiscidae Mitochondrial", alt_name=None, id=33, table={ "TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L", "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "TAT": "Y", "TAC": "Y", "TAA": "Y", # noqa: E241 "TGT": "C", "TGC": "C", "TGA": "W", "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q", "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I", "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K", "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "S", "AGG": "K", "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E", "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G", }, stop_codons=["TAG"], start_codons=["TTG", "CTG", "ATG", "GTG"], ) ######################################################################## # End of auto-generated output from Scripts/update_ncbi_codon_table.py # ########################################################################