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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