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Bio-CUA-1.04
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/ Bio::CUA::CodonTable

NAME

Bio::CUA::CodonTable -- A package processing genetic codon table

SYNOPSIS

This package is provided to improve portability of http://search.cpan.org/dist/Bio-CUA/, in case that one may not install "http://www.bioperl.org/" in BioPerl which includes huge number of modules.

The package obtains genetic code tables from NCBI at http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes

examples:

	# get the standard genetic code
    my $table = Bio::CUA::CodonTable->new(-id => 1)

	# get table from an input file if know genetic codes can not
	# satisfy the need.
	my $table = Bio::CUA::CodonTable->new(-map_file =>
	'codon_to_aa.tsv')
	# in 'codon_to_aa.tsv', it looks like this
	# GCU	A
	# AAU	N
	# CAU	H
	# ...   ...

new

Title   : new
Usage   : $obj = Bio::CUA::CodonTable->new(-map_file => 'file');
Function: creat an object for processing genetic codon tables
Returns : an object of L<Bio::CUA::CodonTable>
Args    : a hash with following keys:
-id
genetic code id. The id follows NCBI's standard, here are
the list:
 1. The Standard Code
 2. The Vertebrate Mitochondrial Code
 3. The Yeast Mitochondrial Code
 4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and
    the Mycoplasma/Spiroplasma Code
 5. The Invertebrate Mitochondrial Code
 6. The Ciliate, Dasycladacean and Hexamita Nuclear Code
 9. The Echinoderm and Flatworm Mitochondrial Code
 10. The Euplotid Nuclear Code
 11. The Bacterial, Archaeal and Plant Plastid Code
 12. The Alternative Yeast Nuclear Code
 13. The Ascidian Mitochondrial Code
 14. The Alternative Flatworm Mitochondrial Code
 16. Chlorophycean Mitochondrial Code
 21. Trematode Mitochondrial Code
 22. Scenedesmus obliquus Mitochondrial Code
 23. Thraustochytrium Mitochondrial Code
 24. Pterobranchia Mitochondrial Code
 25. Candidate Division SR1 and Gracilibacteria Code
 see
 L<http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#SG1>
 for more details.
-map_file
-map_file = a file containing a mapping between codons to amino
acids, one codon per line followed by its amino acid, separated by
tab or space.
-debug
a switch to indicate whether to show more warnings which may
help to identify sources of errors if any. put 1 to switch
it on. The default is off.
Note: argument -map_file has higher priority than -id, and the
default is -id => 1, i.e., the standard genetic code

name

Title   : name
Usage   : $name = $self->name();
Function: the name of genetic code table in use
Returns : a string for the name
Args    : None

id

Title   : id
Usage   : $id = $self->id();
Function: the id of genetic code table in use
Returns : a integer for the id
Args    : None

total_num_of_codons

Title   : total_num_of_codons
Usage   : $num = $self->total_num_of_codons;
Function: get total number of codons of the genetic code table in use
Returns : an integer
Args    : None

is_valid_codon

Title   : is_valid_codon
Usage   : $test = $self->is_valid_codon('ACG');
Function: test whether a given character string is a valid codon in
current codon table
Returns : 1 if true, otherwise 0
Args    : a codon sequence

all_codons

Title   : all_codons
Usage   : @codons = $self->all_codons;
Function: get all the codons in this genetic code table. Codons are
ordered by the coded amino acids. Stop codons are also included.
Returns : an array of codons, or its reference in scalar context
Args    : None

all_sense_codons

Title   : all_sense_codons
Usage   : @codons = $self->all_sense_codons;
Function: get all the sense codons in this genetic code table
Returns : an array of codons, or its reference in scalar context
Args    : None

all_amino_acids

Title   : all_amino_acids
Usage   : @AAs = $self->all_amino_acids
Function: get all the amino acids in this genetic code table. Stop
codons are excluded.
Returns : an array of amino acids, or its reference if in scalar
context
Args    : None

all_start_codons

Title   : all_start_codons
Usage   : @startCodons = $self->all_start_codons;
Function: get all the start codons in the genetic code table in use
Returns : an array of codons, or its reference if in scalar context
Args    : None

all_stop_codons

Title   : all_stop_codons
Usage   : @stopCodons = $self->all_stop_codons;
Function: get all the stop codons in the genetic code table in use
Returns : an array of codons, or its reference if in scalar context
Args    : None

codons_of_AA

Title   : codons_of_AA
Usage   : @codons = $self->codons_of_AA('S');
Function: get codons encoding the given amino acid
Returns : an array of codons, or its reference if in scalar context
Args    : a single amino acid; for stop codons, one can give '*' here

codon_to_AA_map

Title   : codon_to_AA_map
Usage   : $hash = $self->codon_to_AA_map
Function: get the mapping from codon to amino acid in a hash
Returns : a hash reference in which codons are keys and AAs are
values
Args    : None

translate

Title   : translate
Usage   : $AA_string = $self->translate('ATGGCA');
Function: get the translation of input nucleotides
Returns : a string of amino acids, unknown amino acids are
represented as 'X'.
Args    : nucleotide sequence.
Note : if the input sequence is not multiple of 3 long, the last
remained 1 or 2 nucleotides would be simply ignored.

is_stop_codon

Title   : is_stop_codon
Usage   : $test = $self->is_stop_codon('UAG');
Function: check whether this is a stop codon
Returns : 1 if true, otherwise 0
Args    : a codon sequence

codon_degeneracy

 Title   : codon_degeneracy
 Usage   : $hash = $self->codon_degeneracy;
 Function: group AAs and codons into codon degeneracy groups
 Returns : reference to a hash in which 1st level key is degeneracy
 (i.e., 1,2,6,etc), 2nd level key is amino acids for that degeneracy
 group, and 3rd level is reference of arrays containing coding codons
 for each amino acid. For example:

 { 2 => { D => [GAU, GAC],
          C => [UGU, UGC],
		  ...  ...
 		},
   4 => { A => [GCU, GCC, GCA, GCG],
          ...  ...
        },
	...  ...  ...
 }

 Args    : None

AUTHOR

Zhenguo Zhang, <zhangz.sci at gmail.com>

BUGS

Please report any bugs or feature requests to bug-bio-cua at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-CUA. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this module with the perldoc command.

perldoc Bio::CUA::CodonTable

You can also look for information at:

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright 2015 Zhenguo Zhang.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.