[BioSQL-l] *** SPAM *** Re: Storing "per letter" annotation?

[Mark Schreiber]

Hi -

Genbank/EMBL format has options for partial locations that have ends
less than the start or greater than the end of a sequence. This would
let you retain feature information after obtaining a subsequence.

I think these locations can be stored in BioSQL??

- Mark

On 5/25/08, Peter <biopython at maubp.freeserve.co.uk> wrote:
> > It sounds like in essence you want to store alternative sequences in other
> > alphabets for a sequence?
>
> I hadn't thought of it like that, but for many of the examples it
> would just be one character per letter of sequence, so could be held
> as an alternative sequence.  This doesn't really extend to cover
> things like a list of integers or a list of floats, but would
> certainly cover a number of use-cases.
>
> > In BioPerl we have Bio::Seq::SeqWithQuality and the more generic
> > Bio::Seq::MetaI.
>
> I'll have to look at those.
>
> Thanks for you comments Hilmar - I'm not yet sure what would be the
> best way forward for extending BioSQL for this sort of thing.  I guess
> some real world examples of where it would be useful would be a
> helpful guide.
>
> Peter
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