[Biojava-l] SeqIOTools.readEmblNucleotide()?

[Matthew Pocock]

Roy Park wrote:
> As I look at the SeqIOTools.readXXXX() methods, I see that the readEmbl() is
> coded to work only with DNA Alphabets and not RNA Alphabets at all.  I am in
> need of a more generic readEmbl() for nucleotides - i.e. including RNA.  How
> do you suggest on solving this?  Give me some suggestions and directions and
> I'll be glad to write it.  Thanks.
> 
> Roy Park

I may be off-base here, but I think all embl entries, regardless of 
being DNA or RNA store the sequence as DNA letters (t, not u). So, from 
BioJava's point of view, they are all DNA sequences. We could check the 
ID line and translate the DNA to RNA after loading the sequence. Is 
anybody keen on this, or should we continue to treat all EMBL (and I 
guess Genbank) entries as DNA only?

Matthew

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