Mailing Lists

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

Support

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

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

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

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