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

David Messina dmessina at wustl.edu
Sun Nov 12 17:30:59 EST 2006


> The symbols recognized by Bio::Restriction::Enzyme and  
> Bio::Tools::IUPAC
> need to be synchronized. Since 'X' is not recommended by "Nomenclature
> for Incompletely Specified Bases in Nucleic Acid Sequences" (see
> http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it
> stands for xanthine), I am in favor of removing it as a valid symbol.
>
> But I have a feeling that if 'X' is removed as a valid symbol from
> Bio::Tools::IUPAC, this will break a lot of existing code. So the
> simplest solution seems to be to add 'X' to the symbols recognized by
> Bio::Restriction::Enzyme.


How about adding a -strict option which would require valid IUPAC  
symbols (i.e. not 'X')? And the permissive, 'X'-okay behavior would  
be the default.


Dave


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