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Bio::Tools::CodonTableUser Contributed Perl DocumentaBio::Tools::CodonTable(3)

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: April 30, 2013)
	    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

perl v5.24.1			  2017-07-08	     Bio::Tools::CodonTable(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Heikki Lehvaslaiho | APPENDIX

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