[![Build Status](https://travis-ci.org/wang-q/AlignDB-Codon.svg?branch=master)](https://travis-ci.org/wang-q/AlignDB-Codon) [![Coverage Status](http://codecov.io/github/wang-q/AlignDB-Codon/coverage.svg?branch=master)](https://codecov.io/github/wang-q/AlignDB-Codon?branch=master) [![MetaCPAN Release](https://badge.fury.io/pl/AlignDB-Codon.svg)](https://metacpan.org/release/AlignDB-Codon) # NAME AlignDB::Codon - translate sequences and calculate Dn/Ds # DESCRIPTION AlignDB::Codon provides methods to translate sequences and calculate Dn/Ds with different codon tables. Some parts of this module are extracted from BioPerl to avoid the huge number of its dependencies. # METHODS ## change\_codon\_table $obj->change_codon_table(2); Change used codon table and recalc all attributes. Codon table id should be in range of 1-6,9-16,21. ## comp\_codons my ($syn, $nsy) = $obj->comp_codons('TTT', 'GTA'); my ($syn, $nsy) = $obj->comp_codons('TTT', 'GTA', 1); Compares 2 codons to find the number of synonymous and non-synonymous mutations between them. If the third parameter (in 0 .. 2) is given, this method will return syn&nsy at this position. ## is\_start\_codon my $bool = $obj->is_start_codon('ATG') Returns true for codons that can be used as a translation start, false for others. ## is\_ter\_codon my $bool = $obj->is_ter_codon('GAA') Returns true for codons that can be used as a translation terminator, false for others. ## convert\_123 my $three_format = $obj->convert_123('ARN'); Convert aa code from one-letter to three-letter ## convert\_321 my $one_format = $obj->convert_321('AlaArgAsn'); Convert aa code from three-letter to one-letter # AUTHOR Qiang Wang <wang-q@outlook.com> # COPYRIGHT AND LICENSE This software is copyright (c) 2008 by Qiang Wang. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.