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). 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 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. 6. CITATION Zhenguo Zhang and Daven C. Presgraves, CUA: a Flexible Codon Usage Analyzer (In preparation)