[BioSQL-l] Recording "nucleotide" in the sequence table?

[Peter]

On Sun, May 17, 2009 at 12:06 AM, Peter wrote:
> If none of BioPerl, BioJava and BioRuby have an analogous
> sequence representation for a nucleotide sequence which
> might be DNA or RNA, then perhaps the current situation
> with only "protein", "dna", "rna" and "unknown" in the
> biosequence.alphabet field in BioSQL is sufficient.

The original Biopython bug reporter (Bug 2829, David Wyllie)
has replied on the bug.  In his case, rather than using the
generic nucleotide alphabet, he can be a bit more explicit
since he does actually know his sequence is DNA, and this
does get recorded in BioSQL fine.

Given the "nucleotide" alphabet is a corner case in Biopython,
and has no analogue in BioPerl, the status quo is fine. i.e.
The biosequence.alphabet field should contain "dna", "rna",
"protein" or "unknown" (in lower case).

Thanks for your thoughts everyone.

Peter