[Bioperl-l] BioSQL or chado

[Andrew Nunberg]

I am also in the market for a relational schema and found the 
discussion very interesting, but was wondering if  you could "dumb it 
down" for someone who isnt a strong computer person(molec bio turned 
programmer here)

I generate a lot of genomic survery sequences and would like something 
to store the sequences in so that I can
1)store the sequence, boundaries for vector, quality regions, 
annotation features
2)store assemblies of the sequences, annotation features

Our  department would like to be able to use Apollo to view sequences 
for our bench scientists as well as our clients  scientists

I am leaning towards BioSQL only because I most familiar with Bioperl  
and I have incorporated Bioperl into our pipeline.

thanks
Andy

On Tuesday, July 29, 2003, at 07:41 PM, Nathan ((Nat)) Goodman wrote:

> I'm thinking about converting our homegrown relational schema to one 
> of the
> emerging BioPerl-friendly "standard" schemas.  I'm looking for 
> something
> that (1) works now, and (2) is likely to be popular in the BioPerl 
> world for
> some time to come.
>
> I think the choices are BioSQL and chado.  Are there others?  Is one of
> these the obvious right choice?
>
> Thanks,
> Nat
>
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---------------------------------------------------
Andrew Nunberg Ph.D
Bioinfomagician
Orion Genomics
4041 Forest Park
St Louis, MO
314-615-6989
anunberg at oriongenomics.com
www.oriongenomics.com