1. Bio-CUA

This is a Perl software package for analyzing codon usage bias.

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

metrics 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). Biased codon

usage is widespread, visible in all species. It is important both to

identify codons having high translational efficiency (often termed

optimal codons) and to study the distribution of codon usage among

genes (e.g., genes with more optimal codons versus genes with fewer

optimal codons).

So far, no software implements all the above CUB metrics in one place.

More importantly, parameters in existing software are often fixed,

so one can compute certain types of CUB metrics for a limited list of

species and cannot tune parameters. For example, when one wants to

identify optimal codons in certain tissues, it may be better to use

most highly expressed genes of that tissue to calculate CAI, which is

impossible with existing software.

This package mainly solves these two problems: providing tools

computing all common CUB metrics and allowing users to tune parameters

freely. We also incorporate or extend some method variants, such as

GC-content corrected ENC, background-data normalized CAI, etc.

See the relevant methods' description in CUB classes for more details.

3. INSTALLATION

To install this module, run the following commands:

a. If install after downloading the package,

perl Makefile.PL

make

make test

make install

b. 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 find a tutorial on the CPAN, which is also accessible

through

perldoc Bio::CUA::Tutorial

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/

You can also email me at zhangz.sci@gmail.com for help.

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/>.

6. CITATION

Zhenguo Zhang, CUA: a Flexible and

Comprehensive Codon Usage Analyzer (In preparation)