[GMOD-devel] Re: [Open-bio-l] Schema for genes & features & mappings to assemblies

[Lincoln Stein]

> One thing to remeber with zero-level type arrangements: you're
> potentially going to want to store whole chromosome sequences.
> A lot of databases will not be happy about this, especially if you
> then want to go back and efficiently pull out a small region
> from the middle of chromosome 1.

Absolutely.  I've got the whole of human chromosome 1 in a Bio::DB::GFF 
database.  The trick is to store it in 2000 K segments with an offset and 
then to have SQL automagically turn it back into whatever contiguous region 
you want.  You can do this with a stored procedure, or with a bit of client 
code.
>
> One solution would be to have a new sequence-storage type in BioSQL
> (an alternative to the existing biosequence table), which stores
> the sequence in "shredded" (small chunks) form.  This is different
> from assemblies, in that the use of shredded sequence behind
> the scenes should be completely hidden from the user.  I remember
> talking to someone (Lincoln, I think) about this at Cape Town.

Oh gosh.  I'm responding to the e-mail without reading it through.  Yes, 
Thomas, absolutely!  And it was probably me you were talking to.

Lincoln

>
>
>     Thomas.
>
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