Bio::Tools::CodonTable(3p)

NAME
Bio::Tools::CodonTable - Codon table object

SYNOPSIS
  # This is a read-only class for all known codon tables.  The IDs are
  # the ones used by nucleotide sequence databases.  All common IUPAC
  # ambiguity codes for DNA, RNA and amino acids are recognized.

  use Bio::Tools::CodonTable;

  # defaults to ID 1 "Standard"
  $myCodonTable   = Bio::Tools::CodonTable->new();
  $myCodonTable2  = Bio::Tools::CodonTable->new( -id => 3 );

  # change codon table
  $myCodonTable->id(5);

  # examine codon table
  print  join (' ', "The name of the codon table no.", $myCodonTable->id(4),
           "is:", $myCodonTable->name(), "\n");

  # print possible codon tables
  $tables = Bio::Tools::CodonTable->tables;
  while ( ($id,$name) = each %{$tables} ) {
    print "$id = $name\n";
  }

  # translate a codon
  $aa = $myCodonTable->translate('ACU');
  $aa = $myCodonTable->translate('act');
  $aa = $myCodonTable->translate('ytr');

  # reverse translate an amino acid
  @codons = $myCodonTable->revtranslate('A');
  @codons = $myCodonTable->revtranslate('Ser');
  @codons = $myCodonTable->revtranslate('Glx');
  @codons = $myCodonTable->revtranslate('cYS', 'rna');

  # reverse translate an entire amino acid sequence into a IUPAC
  # nucleotide string

  my $seqobj    = Bio::PrimarySeq->new(-seq => 'FHGERHEL');
  my $iupac_str = $myCodonTable->reverse_translate_all($seqobj);

  # boolean tests
  print "Is a start\n"       if $myCodonTable->is_start_codon('ATG');
  print "Is a terminator\n"  if $myCodonTable->is_ter_codon('tar');
  print "Is a unknown\n"     if $myCodonTable->is_unknown_codon('JTG');

DESCRIPTION
Codon tables are also called translation tables or genetic codes since that is what they represent. A bit more complete picture of the full complexity of codon usage in various taxonomic groups is presented at the NCBI Genetic Codes Home page.

CodonTable is a BioPerl class that knows all current translation tables that are used by primary nucleotide sequence databases (GenBank, EMBL and DDBJ). It provides methods to output information about tables and relationships between codons and amino acids.

This class and its methods recognized all common IUPAC ambiguity codes for DNA, RNA and animo acids. The translation method follows the conventions in EMBL and TREMBL databases.

It is a nuisance to separate RNA and cDNA representations of nucleic acid transcripts. The CodonTable object accepts codons of both type as input and allows the user to set the mode for output when reverse translating. Its default for output is DNA.

Note:

This class deals primarily with individual codons and amino acids. However in the interest of speed you can translate longer sequence, too. The full complexity of protein translation is tackled by Bio::PrimarySeqI::translate.

The amino acid codes are IUPAC recommendations for common amino acids:

          A           Ala            Alanine
          R           Arg            Arginine
          N           Asn            Asparagine
          D           Asp            Aspartic acid
          C           Cys            Cysteine
          Q           Gln            Glutamine
          E           Glu            Glutamic acid
          G           Gly            Glycine
          H           His            Histidine
          I           Ile            Isoleucine
          L           Leu            Leucine
          K           Lys            Lysine
          M           Met            Methionine
          F           Phe            Phenylalanine
          P           Pro            Proline
          O           Pyl            Pyrrolysine (22nd amino acid)
          U           Sec            Selenocysteine (21st amino acid)
          S           Ser            Serine
          T           Thr            Threonine
          W           Trp            Tryptophan
          Y           Tyr            Tyrosine
          V           Val            Valine
          B           Asx            Aspartic acid or Asparagine
          Z           Glx            Glutamine or Glutamic acid
          J           Xle            Isoleucine or Valine (mass spec ambiguity)
          X           Xaa            Any or unknown amino acid

It is worth noting that, "Bacterial" codon table no. 11 produces an polypeptide that is, confusingly, identical to the standard one. The only differences are in available initiator codons.

NCBI Genetic Codes home page:
     (Last update of the Genetic Codes: Nov. 18, 2016)
     https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c

ASN.1 version with ids 1 to 25 is at:
     ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt

Thanks to Matteo diTomasso for the original Perl implementation of these tables.

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho
Email: heikki-at-bioperl-dot-org

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  id
 Title   : id
 Usage   : $obj->id(3); $id_integer = $obj->id();
 Function: Sets or returns the id of the translation table.  IDs are
           integers from 0 (special ATG-only start) to 25, excluding
           7-8 and 17-20 which have been removed. If an invalid ID is
           given the method returns 1, the standard table.
 Example :
 Returns : value of id, a scalar, warn and fall back to 1 (standard table)
           if specified id is not valid
 Args    : newvalue (optional)

  name
 Title   : name
 Usage   : $obj->name()
 Function: returns the descriptive name of the translation table
 Example :
 Returns : A string
 Args    : None

  tables
 Title   : tables
 Usage   : $obj->tables()  or  Bio::Tools::CodonTable->tables()
 Function: returns a hash reference where each key is a valid codon
           table id() number, and each value is the corresponding
           codon table name() string
 Example :
 Returns : A hashref
 Args    : None

  translate
 Title   : translate
 Usage   : $obj->translate('YTR')
 Function: Returns a string of one letter amino acid codes from
           nucleotide sequence input. The imput can be of any length.

           Returns 'X' for unknown codons and codons that code for
           more than one amino acid. Returns an empty string if input
           is not three characters long. Exceptions for these are:

             - IUPAC amino acid code B for Aspartic Acid and
               Asparagine, is used.
             - IUPAC amino acid code Z for Glutamic Acid, Glutamine is
               used.
             - if the codon is two nucleotides long and if by adding
               an a third character 'N', it codes for a single amino
               acid (with exceptions above), return that, otherwise
               return empty string.

           Returns empty string for other input strings that are not
           three characters long.

 Example :
 Returns : a string of one letter ambiguous IUPAC amino acid codes
 Args    : ambiguous IUPAC nucleotide string

  translate_strict
 Title   : translate_strict
 Usage   : $obj->translate_strict('ACT')
 Function: returns one letter amino acid code for a codon input

           Fast and simple translation. User is responsible to resolve
           ambiguous nucleotide codes before calling this
           method. Returns 'X' for unknown codons and an empty string
           for input strings that are not three characters long.

           It is not recommended to use this method in a production
           environment. Use method translate, instead.

 Example :
 Returns : A string
 Args    : a codon = a three nucleotide character string

  revtranslate
 Title   : revtranslate
 Usage   : $obj->revtranslate('G')
 Function: returns codons for an amino acid

           Returns an empty string for unknown amino acid
           codes. Ambiguous IUPAC codes Asx,B, (Asp,D; Asn,N) and
           Glx,Z (Glu,E; Gln,Q) are resolved. Both single and three
           letter amino acid codes are accepted. '*' and 'Ter' are
           used for terminator.

           By default, the output codons are shown in DNA.  If the
           output is needed in RNA (tr/t/u/), add a second argument
           'RNA'.

 Example : $obj->revtranslate('Gly', 'RNA')
 Returns : An array of three lower case letter strings i.e. codons
 Args    : amino acid, 'RNA'

  reverse_translate_all
 Title   : reverse_translate_all
 Usage   : my $iup_str = $cttable->reverse_translate_all($seq_object)
           my $iup_str = $cttable->reverse_translate_all($seq_object,
                                                         $cutable,
                                                         15);
 Function: reverse translates a protein sequence into IUPAC nucleotide
           sequence. An 'X' in the protein sequence is converted to 'NNN'
           in the nucleotide sequence.
 Returns : a string
 Args    : a Bio::PrimarySeqI compatible object (mandatory)
           a Bio::CodonUsage::Table object and a threshold if only
             codons with a relative frequency above the threshold are
             to be considered.

  reverse_translate_best
 Title   : reverse_translate_best
 Usage   : my $str = $cttable->reverse_translate_best($seq_object,$cutable);
 Function: Reverse translates a protein sequence into plain nucleotide
           sequence (GATC), uses the most common codon for each amino acid
 Returns : A string
 Args    : A Bio::PrimarySeqI compatible object and a Bio::CodonUsage::Table object

  is_start_codon
 Title   : is_start_codon
 Usage   : $obj->is_start_codon('ATG')
 Function: returns true (1) for all codons that can be used as a
           translation start, false (0) for others.
 Example : $myCodonTable->is_start_codon('ATG')
 Returns : boolean
 Args    : codon

  is_ter_codon
 Title   : is_ter_codon
 Usage   : $obj->is_ter_codon('GAA')
 Function: returns true (1) for all codons that can be used as a
           translation tarminator, false (0) for others.
 Example : $myCodonTable->is_ter_codon('ATG')
 Returns : boolean
 Args    : codon

  is_unknown_codon
 Title   : is_unknown_codon
 Usage   : $obj->is_unknown_codon('GAJ')
 Function: returns false (0) for all codons that are valid,
        true (1) for others.
 Example : $myCodonTable->is_unknown_codon('NTG')
 Returns : boolean
 Args    : codon

  unambiguous_codons
 Title   : unambiguous_codons
 Usage   : @codons = $self->unambiguous_codons('ACN')
 Returns : array of strings (one-letter unambiguous amino acid codes)
 Args    : a codon = a three IUPAC nucleotide character string

  _unambiquous_codons
deprecated, now an alias for unambiguous_codons

  add_table
 Title   : add_table
 Usage   : $newid = $ct->add_table($name, $table, $starts)
 Function: Add a custom Codon Table into the object.
           Know what you are doing, only the length of
           the argument strings is checked!
 Returns : the id of the new codon table
 Args    : name, a string, optional (can be empty)
           table, a string of 64 characters
           startcodons, a string of 64 characters, defaults to standard