[Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC

Brian Osborne bosborne11 at verizon.net
Tue Nov 14 16:54:25 EST 2006


The typical solution is to declare an alphabet, as in:

my $seq = Bio::Seq->new(-seq => "xxxx", -alphabet => "dna")

Then Bioperl will not check your sequence. This works since you'll know that
the alphabet, in this case, has to be "dna".

Brian O.

On 11/12/06 1:11 PM, "Conrad Halling" <chhalling at verizon.net> wrote:

> This test fails because Bio::Tools::IUPAC module includes 'X' as a valid
> base symbol, whereas Bio::Restriction::Enzyme does not.

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