[BioSQL-l] BioSQL seqeunce quality tables

[Dan Kortschak]

I was mainly thinking of contigs, but it was more an exploratory think.

cheers
Dan

On Tue, 2010-11-23 at 09:00 +0000, Peter wrote:
> For Biopython we decided not to store the quality, and document this
> as a known limitation. As I recall there was some discussion about
> using the existing BioSQL feature annotations and using a (Sanger)
> FASTQ encoded string was suggested, but there was no consensus.
> 
> Is there actually a need for this? You can't be thinking of storing
> raw
> reads in BioSQL (are you? I think you'll be disappointed with the
> performance), but perhaps it is reasonable for contigs.
> 
> I was also interested in other per-letter-annotation, like secondary
> structure predictions (which can be stored as a string with the same
> length as the sequence) or more general things like atomic coords.
> In principle new tables could be introduced to BioSQL just for
> per-letter-annotation, designed to work well with extracting a
> subsequence with the relevant sub-set of per-letter-annotation.
> 
> Peter