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:
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
EBI Translation Table Viewer:
http://www.ebi.ac.uk/cgi-bin/mutations/trtables.cgi
Amended ASN.1 version with ids 16 and 21 is at:
ftp://ftp.ebi.ac.uk/pub/databases/geneticcode/
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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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-orgAPPENDIX
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 1 to 15, excluding 7 and 8 which have been removed as redundant. If an invalid ID is given the method returns 0, false. Example : Returns : value of id, a scalar, 0 if not a 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_codonsadd_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