[BioSQL-l] very new to biosql--sequence loading question

[Richard HOLLAND]

Hi,

I can't answer the MySQL error question as I don't know anything about it, but I'm curious as to the differences between your db and BioSQL. What was it that BioSQL could not do that you had to reimplement in a different way? Maybe some suggestions could be made for improvements to BioSQL? Or maybe BioSQL can actually help with the problem but in a way that wasn't immediately obvious?

cheers,
Richard


-----Original Message-----
From:	biosql-l-bounces at portal.open-bio.org on behalf of Renee Halbrook
Sent:	Wed 6/22/2005 11:24 PM
To:	biosql-l at open-bio.org
Cc:	
Subject:	[BioSQL-l] very new to biosql--sequence loading question

Hi,

I am very new to biosql. I have designed a mysql
schema to represent cyanobacteria, pulled from genbank
files. It is not identical to the biosql schema, but
it is similar.

My specific issue is in loading large sequences into a
sequence table, (essentially identical to the
biosequence table) using perl dbi. I keep running into
a 'max_allowed_packet' issue, even though I have
bumped it up to a 1 gig in the my.cnf file.

I would like to see how other people have implemented
this.

Could someone please point me in the direction of the
documentation for loading sequences using perl, from
flat genbank files, into a mysql database ?

Thanks in advance for any help.

Regards,
Renee



		
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