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). Biased codon usage is widespread, visible in all species. It is important both to identify codons having high translational efficiency (often named 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 exists to compute all the above CUB indices, and it is worse that parameters in existing software are often fixed, so one can compute certain types of CUB indices for a limited list of species and can not modify parameters. For example, when one wants to identify optimal codons in certain tissues, it may be better to use most highly expressed genes to calculate CAI index, which is impossible with existing software.

This package mainly solves these two problems: providing tools computing all common CUB indices 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:

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/

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 Lhttp://www.gnu.org/licenses/.