1. Bio-CUA

Version: 1.01

2. Purpose

The aim of this distribution is to provide comprehensive and flexible
tools to analyze codon usage bias (CUB) and relevant problems.

One amino acid can be encoded by more than one synonymous codon, and
synonymous codons are unevenly used. For example, some codons are used
more often than other synonymous ones in highly expressed genes
(I<Sharp and Li 1987>). To measure the unevenness of codon usage, multiple
indices of codon usage bias have been developed, such as Fop
(Frequency of optimal codons), CAI (Codon Adaptation Index), tAI (tRNA
Adaptation Index), and ENC (Effective Number of Codons). The causes of
CUB phenomena are complicated, including, mutational bias, selection
on translational efficiency or accurancy. CUB is one fundamental concept
in genetics.

So far, no software exists to compute all the above CUB indices, and
worse is that parameters of CUB calculations are often fixed in
software, so one can only analyze genes in a limited list of species
and one can not incorporate its own parameters such as sequences of
highly expressed genes in a tissue.

This package mainly solves these two problems. We also extend some
methods, such as GC-content corrected ENC, background-data normalized
CAI, etc. See the relevant methods in CUB classes for more details.


3. INSTALLATION

To install this module, run the following commands:

	perl Makefile.PL
	make
	make test
	make install

or install directly from CPAN as
	cpan Bio::CUA

4. SUPPORT AND DOCUMENTATION

After installing, you can find documentation for this module 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/


5. LICENSE AND COPYRIGHT

Copyright (C) 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 L<http://www.gnu.org/licenses/>.