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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/.