NAME
build_tai_param.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 build_tai_param.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 build_tai_param.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)
AnnoCPAN: Annotated CPAN documentation
CPAN Ratings
Search CPAN
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/.