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| # CUA | ||
| A software package for Codon Usage Analyses | ||
| 1. Bio-CUA | ||
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| This is a software package designed to analyse codon usage in protein-coding sequences. The usage of codons often varies for gene to gene and from organism to organism. To measure the variation, different parameters have been developed. The most often used codon usage bias parameters are as follows: | ||
| 1. CAI: Codon Adaptation Index | ||
| 2. Fop: Frequency of optimal codons | ||
| 3. tAI: tRNA Adaptation Index | ||
| 4. ENC: Effective Number of Codons. | ||
| Version: 1.01 | ||
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| In addition to implementing all the parameters in this package, the most value feature of this package is its flexibility in specifying user-specific parameters such as the list of optimal codons, the abundance of tRNAs, genetic codon table, etc. | ||
| 2. Purpose | ||
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| Please email me at zhangz.sci@gmail.com if you have any questions. Your input is always welcome. | ||
| The aim of this distribution is to provide comprehensive and flexible | ||
| tools to analyze codon usage bias (CUB) and relevant problems. | ||
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| Enjoy computation! | ||
| 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). | ||
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| # some changes for testing connection | ||
| 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. | ||
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| 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. | ||
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| 3. INSTALLATION | ||
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| To install this module, run the following commands: | ||
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| perl Makefile.PL | ||
| make | ||
| make test | ||
| make install | ||
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| or install directly from CPAN as | ||
| cpan Bio::CUA | ||
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| 4. SUPPORT AND DOCUMENTATION | ||
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| After installing, you can find documentation for this module with the | ||
| perldoc command. | ||
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| perldoc Bio::CUA | ||
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| You can also look for information at: | ||
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| RT, CPAN's request tracker (report bugs here) | ||
| http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-CUA | ||
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| AnnoCPAN, Annotated CPAN documentation | ||
| http://annocpan.org/dist/Bio-CUA | ||
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| CPAN Ratings | ||
| http://cpanratings.perl.org/d/Bio-CUA | ||
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| Search CPAN | ||
| http://search.cpan.org/dist/Bio-CUA/ | ||
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| You can also email me at zhangz.sci@gmail.com for help. | ||
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| 5. LICENSE AND COPYRIGHT | ||
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| Copyright (C) 2015 Zhenguo Zhang | ||
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| 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. | ||
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| 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. | ||
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| 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/>. | ||
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| again testing on connection |