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Validating Installation of a GenBank data release in GCG

Staffa.Nick staffa at niehs.nih.gov
Thu Jun 6 07:33:34 EST 2002


I usually do a lookup on genbank and est1, est2 et c. 
Something simple just to see that it is working. 
The new paged system makes life easier.  
I used to randomly pick a sequence out of any new EST section and try to find it
with LookUp. 
This is not an extensive test,  but that's why we have users. 

I don't make local blast databases of Genbank.

I have not automated the process beyond being able to download as many sections
as I desire with one batch submission. 
I divide the process into Genbank, GSS, HTG, EST1 EST2.   If the connection
breaks,  I edit the C-shell scripts and start from the last completed section. 
These scripts are modifications of the get_gbnew script supplied by GCG.

A perl script that reads the release notes and fetches all the sections would
seem to be the next step in automation.  
Maybe you have some whiz-bang programmers who can turn out the appropriate
scripts faster than modifying the dinosaurs I use. 

  

Nick Staffa
Telephone: 919-316-4569  (NIEHS: 6-4569)
Scientific Computing Support Group
NIEHS Information Technology Support Services Contract
National Institute of Environmental Health Sciences
Research Triangle Park, North Carolina
Debra Parrish, DIR monitor.



> ----------
> From: 	mem at jax.org
> Sent: 	Wednesday, June 5, 2002 12:00 PM
> To: 	info-gcg at hgmp.mrc.ac.uk
> Subject: 	Validating Installation of a GenBank data release in GCG
> 
> Hi,
> As you all know, installing a GenBank release in the GCG system is a 
> complicated affair. We are in the process of developing a test plan for 
> testing a newly installed data release.
> 
> I am wondering if anyone has any experience to share about testng the
> soundness
> of a newly installed release, i.e., testing LookUp, for example to ensure 
> you get appropriate results, testing BLAST to see that you get all and only 
> the appropriate matching sequences.
> 
> Thanks.
> 
> Marge
> Marge May
> mem at jax.org, 207-288-6630
> Software Engineer
> Computational Biology Dept.,
> The Jackson Laboratory
> Bar Harbor, Maine
> 
> ---
> 
> 

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