NAME
Bio::Tools::CodonOptTable - A more elaborative way to check the codons quality
VERSION
Version 0.01
SYNOPSIS
We produces each codon frequency, Relative Synonymous Codons Uses and Relative Adaptiveness of a Codon table and bar graph
that will help you to calculate the Codon Adaptation Index (CAI) of a gene, to see the gene expression level.
Perhaps a little code snippet.
my
$seqobj
= Bio::Tools::CodonOptTable->new (
-seq
=>
'ATGGGGTGGGCACCATGCTGCTGTCGTGAATTTGGGCACGATGGTGTACGTGCTCGTAGCTAGGGTGGGTGGTTTG'
,
-id
=>
'GeneFragment-12'
,
-accession_number
=>
'Myseq1'
,
-alphabet
=>
'dna'
,
-is_circular
=> 1
);
#If you wanna read from file
my
$seqobj
= Bio::Tools::CodonOptTable->new(
-file
=>
"contig.fasta"
,
-format
=>
'Fasta'
);
#If you have Accession number and want to get file from NCBI
my
$seqobj
= Bio::Tools::CodonOptTable->new(
-ncbi_id
=>
"J00522"
);
my
$myCodons
=
$seqobj
->rscu_rac_table();
if
(
$myCodons
)
{
for
my
$a
(
@$myCodons
)
{
"Codon : "
,
$each_aa
->[1]->{
'codon'
},
"\t"
;
"Frequency : "
,
$each_aa
->[1]->{
'frequency'
},
"\t"
;
"AminoAcid : "
,
$each_aa
->[1]->{
'aa_name'
},
"\t"
;
"RSCU Value : "
,
$each_aa
->[1]->{
'rscu'
},
"\t"
;
#Relative Synonymous Codons Uses
"RAC Value : "
,
$each_aa
->[1]->{
'rac'
},
"\t"
;
#Relative Adaptiveness of a Codon
"\n"
;
}
}
# to produce a graph between RSCU & RAC
# Graph output file extension should be GIF, we support GIF only
$seqobj
->generate_graph(
$myCodons
,
"myoutput.gif"
);
...
METHODS
Title : new
Usage1 :
$seq
= Bio::Tools::CodonOptTable->new(
-seq
=>
'ATGGGGGTGGTGGTACCCT'
,
-id
=>
'human_id'
,
-accession_number
=>
'AL000012'
,
);
Usage2 :
$seq
= Bio::Tools::CodonOptTable->new(
-file
=>
'myseq.fasta'
,
-format
=>
'fasta'
,
);
Usage3 :
$seq
= Bio::Tools::CodonOptTable->new(
-ncbi_id
=>
'J00522'
);
Function: Returns a new primary seq object from
basic constructors, being a string
for
the sequence
and strings
for
id and accession_number.
Returns : a new Bio::PrimarySeq object
Args :
-seq
=> sequence string
-display_id
=> display id of the sequence (locus name)
-accession_number
=> accession number
-primary_id
=> primary id (Genbank id)
-desc
=> description text
-alphabet
=> molecule type (dna,rna,protein)
-id
=> alias
for
display id
-file
=> file location
-format
=> file
format
-ncbi_id
=> NCBI accession number
Note : IF you are reading sequence from file it will call _read_localfile method
IF you are fetching file form NCBI it will call _read_remotefile method
METHODS
Title : calculate_rscu
Function: Calculate the RSCU(Relative Synonymous Codons Uses).
Note : The formula is used in the following references.
METHODS
Title : calculate_rac
Function: Calculate the RAC(Relative Adaptiveness of a Codon).
Note : The formula is used in the following references.
METHODS
Title : generate_graph
Function: Produce a bar graph between RAC(Relative Adaptiveness of a Codon) & RSCU(Relative Synonymous Codons Uses).
AUTHOR
Rakesh Kumar Shardiwal, <rakesh.shardiwal at gmail.com>
BUGS
Please report any bugs or feature requests to bug-bio-tools-codonopttable at rt.cpan.org
, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Tools-CodonOptTable. 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::Tools::CodonOptTable
You can also look for information at:
RT: CPAN's request tracker
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Tools-CodonOptTable
AnnoCPAN: Annotated CPAN documentation
CPAN Ratings
Search CPAN
ACKNOWLEDGEMENTS
Lalchand Kumawat <lalchand82@gmail.com> Rajneesh Kumar Sharma <biorajneesh@gmail.com>
COPYRIGHT & LICENSE
Copyright 2008 Rakesh Kumar Shardiwal, all rights reserved.
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.