Validating Installation of a GenBank data release in GCG

David Mathog mathog at caltech.edu
Thu Jun 6 10:51:53 EST 2002

Marge May wrote:
> 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.

I suggest that you try to fetch the first and last entries in the database
and also run something like:

  % findpatterns -infile=database:\* -pattern=WWW -outfile=test.find

where WWW is a pattern which will have a few matches, but not too
many since the goal is just to test read the sequences.  If the fetch's
come back with reference and sequence and the findpatterns works then
pretty much everything else should work as well.

If you're EMBOSS indexing these databases as well apply the same
tests there using seqret and fuzzpro or fuzznuc.


David Mathog
mathog at caltech.edu

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