Lab database: new user questions

Keith James bss194 at pwilliams.bangor.ac.uk
Thu Oct 29 10:32:57 EST 1998


I'm using ACeDB to set up a database for our lab along the lines of
that available as part of Brain Fristensky's Birch package. I'm
running on Linux and have got as far as compiling ACeDB 4.5e and
writing some new models to suit our purposes. We will only need a
small subset of the default models.wrm, I think.

I've read lots of documentation and been through Dejanews etc., but I
am still unsure of a couple of points.

Firstly, how to enter restriction enzymes to enable searching by
enzyme name rather than typing in the site. I can enter them, but the
search still complains that my keyset contains no oligos or enzymes,
so I am doing something wrong. My motifs class looks like the standard
one. I'd also like to be able to search for oligos in the same way.

I found a pointer to an ace file of enzymes which sadly was no longer
there when I looked. I presume the elegans data itself contains this,
but it's a big download. Is there any documentation specifically on
how the motif/oligo/restriction model and search work?

Secondly, when blast searching the system complains about not finding
the blast script. I've checked obvious things like its presence in the
wscripts directory and its file permissions. What else should I look
for?

Any references and/or advice would be welcome.

-- 
Keith James  --  k.james at bangor.ac.uk  --  http://www.bangor.ac.uk/~bss194 
Biodegradation Group - School of Biological Sciences - University of Wales
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