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.