NAME

tai_codon.pl - a program to calculate tAI of each codon

VERSION

VERSION: 0.01

SYNOPSIS

This program calculates tAI (tRNA adaptaion index) at codon level, which is part of distribution http://search.cpan.org/dist/Bio-CUA/

# calculate tAI for drosophila melanogaster tai_codon.pl -t dmel_tRNA_copy_number.tsv -o dmel_tAI.tsv

# one can get tRNA copy numbers from the database # GtRNADB

OPTIONS

Mandatory options:

-t/--tRNA

the file containing tRNA abundance in the format:

        anti-codon1<tab>3
        anti-codon1<tab>6
        ...   ...

each line contains one anticodon followed by the total copy number of tRNAs harboring this anticodon.

Auxiliary options:

-g/--gc-id

ID of genetic code table. Used for mapping between codons and amino acids.

-o/--out-file

the file to store the result. Default is standard output.

-h/--help

show this help message. For more detailed information, run 'perldoc tai_codon.pl'

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 class with the perldoc command.

        perldoc Bio::CUA

You can also look for information at:

• RT: CPAN's request tracker (report bugs here)

  http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-CUA

• AnnoCPAN: Annotated CPAN documentation

  http://annocpan.org/dist/Bio-CUA

• CPAN Ratings

  http://cpanratings.perl.org/d/Bio-CUA

• Search CPAN

  http://search.cpan.org/dist/Bio-CUA/

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/.