Bio::CodonUsage::Table - for access to the Codon usage Database at
http://www.kazusa.or.jp/codon.
use Bio::CodonUsage::Table;
use Bio::DB::CUTG;
use Bio::CodonUsage::IO;
use Bio::Tools::SeqStats;
# Get a codon usage table from web database
my $cdtable = Bio::DB::CUTG->new(-sp => 'Mus musculus',
-gc => 1);
# Or from local file
my $io = Bio::CodonUsage::IO->new(-file => "file");
my $cdtable = $io->next_data();
# Or create your own from a Bio::PrimarySeq compliant object,
# $codonstats is a ref to a hash of codon name /count key-value pairs
my $codonstats = Bio::Tools::SeqStats->count_codons($Seq_objct);
# '-data' must be specified, '-species' and 'genetic_code' are optional
my $CUT = Bio::CodonUsage::Table->new(-data => $codonstats,
-species => 'Hsapiens_kinase');
print "leu frequency is ", $cdtable->aa_frequency('LEU'), "\n";
print "freq of ATG is ", $cdtable->codon_rel_frequency('ttc'), "\n";
print "abs freq of ATG is ", $cdtable->codon_abs_frequency('ATG'), "\n";
print "number of ATG codons is ", $cdtable->codon_count('ATG'), "\n";
print "GC content at position 1 is ", $cdtable->get_coding_gc('1'), "\n";
print "total CDSs for Mus musculus is ", $cdtable->cds_count(), "\n";
This class provides methods for accessing codon usage table data.
All of the methods at present are simple look-ups of the table or are derived
from simple calculations from the table. Future methods could include
measuring the codon usage of a sequence , for example, or provide methods for
examining codon usage in alignments.
Bio::Tools::CodonTable, Bio::WebAgent, Bio::CodonUsage::IO, Bio::DB::CUTG
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modules. Send your comments and suggestions preferably to one of the Bioperl
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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.
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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : new
Usage : my $cut = Bio::CodonUsage::Table->new(-data => $cut_hash_ref,
-species => 'H.sapiens_kinase'
-genetic_code =>1);
Returns : a reference to a new Bio::CodonUsage::Table object
Args : none or a reference to a hash of codon counts. This constructor is
designed to be compatible with the output of
Bio::Tools::SeqUtils::count_codons()
Species and genetic code parameters can be entered here or via the
species() and genetic_code() methods separately.
Title : all_aa_frequencies
Usage : my $freq = $cdtable->all_aa_frequencies();
Returns : a reference to a hash where each key is an amino acid
and each value is its frequency in all proteins in that
species.
Args : none
Title : codon_abs_frequency
Usage : my $freq = $cdtable->codon_abs_frequency('CTG');
Purpose : To return the frequency of that codon as a percentage
of all codons in the organism.
Returns : a percentage frequency
Args : a non-ambiguous codon string
Title : codon_rel_frequency
Usage : my $freq = $cdtable->codon_rel_frequency('CTG');
Purpose : To return the frequency of that codon as a percentage
of codons coding for the same amino acid. E.g., ATG and TGG
would return 100 as those codons are unique.
Returns : a percentage frequency
Args : a non-ambiguous codon string
Title : probable_codons
Usage : my $prob_codons = $cd_table->probable_codons(10);
Purpose : to obtain a list of codons for the amino acid above a given
threshold % relative frequency
Returns : A reference to a hash where keys are 1 letter amino acid codes
and values are references to arrays of codons whose frequency
is above the threshold.
Arguments: a minimum threshold frequency
Title : most_common_codons
Usage : my $common_codons = $cd_table->most_common_codons();
Purpose : To obtain the most common codon for a given amino acid
Returns : A reference to a hash where keys are 1 letter amino acid codes
and the values are the single most common codons for those amino acids
Arguments: None
Title : codon_count
Usage : my $count = $cdtable->codon_count('CTG');
Purpose : To obtain the absolute number of the codons in the
organism.
Returns : an integer
Args : a non-ambiguous codon string
Title : get_coding_gc
Usage : my $count = $cdtable->get_coding_gc(1);
Purpose : To return the percentage GC composition for the organism at
codon positions 1,2 or 3, or an average for all coding sequence
('all').
Returns : a number (%-age GC content) or 0 if these fields are undefined
Args : 1,2,3 or 'all'.
Title : set_coding_gc
Usage : my $count = $cdtable->set_coding_gc(-1=>55.78);
Purpose : To set the percentage GC composition for the organism at
codon positions 1,2 or 3, or an average for all coding sequence
('all').
Returns : void
Args : a hash where the key must be 1,2,3 or 'all' and the value the %age GC
at that codon position..
Title : species
Usage : my $sp = $cut->species();
Purpose : Get/setter for species name of codon table
Returns : Void or species name string
Args : None or species name string
Title : genetic_code
Usage : my $sp = $cut->genetic_code();
Purpose : Get/setter for genetic_code name of codon table
Returns : Void or genetic_code id, 1 by default
Args : None or genetic_code id, 1 by default if invalid argument.
Title : cds_count
Usage : my $count = $cdtable->cds_count();
Purpose : To retrieve the total number of CDSs used to generate the Codon Table
for that organism.
Returns : an integer
Args : none (if retrieving the value) or an integer( if setting ).
Title : aa_frequency
Usage : my $freq = $cdtable->aa_frequency('Leu');
Purpose : To retrieve the frequency of an amino acid in the organism
Returns : a percentage
Args : a 1 letter or 3 letter string representing the amino acid
Title : common_codon
Usage : my $freq = $cdtable->common_codon('Leu');
Purpose : To retrieve the frequency of the most common codon of that aa
Returns : a percentage
Args : a 1 letter or 3 letter string representing the amino acid
Title : rare_codon
Usage : my $freq = $cdtable->rare_codon('Leu');
Purpose : To retrieve the frequency of the least common codon of that aa
Returns : a percentage
Args : a 1 letter or 3 letter string representing the amino acid