Lookup indices & native SRS

Peter Rice pmr at sanger.ac.uk
Thu Jun 27 04:11:34 EST 1996


In article <1996Jun26.121100.235 at immunbio.mpg.de> GARTMANN at IMMUNBIO.MPG.DE (Christoph Gartmann) writes:

>I think this question has been addressed before but I couldn't find
>it anymore.
>
>So, is it possible to use the LookUp indices provided by GCG under
>SRS V4.08?

Yes, but I don't think you would want to.

GCG's indices have no links to databases like PROSITE (actually, they
don't even index prosite).

A more reasonable question is "can I use my normal SRS 4.08 indices
with GCG?" to which the answer is "yes, but GCG doesn't make it easy."

There are two fixes. One posted here some time ago by Reinhard Doelz,
and another which I have hacked together here but not used much (I
tell users to use getz instead of "LookUp" as GCG's LookUp makes no
use of most of SRS anyway.

The basic problem is that with all the usual SRS indices, GCG's menu
blows up - also, GCG assumes that all SRS indexed databases are
sequence ones. So, basically you have to tell LookUp to only
use the sequence databases and ignore the rest.

Oh yes, you also have to watch out for all those duplicated commands
that GCG didn't rename: srsbuild, srscheck, odd

I suggest keeping users away from LookUp, otherwise when SRS 5 and
GCG 9 come along you could have an interesting time fixing it all over
again.

--
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Peter Rice                           | Informatics Division,
E-mail: pmr at sanger.ac.uk             | The Sanger Centre,
Tel: (44) 1223 494967                | Wellcome Trust Genome Campus,
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URL: http://www.sanger.ac.uk/~pmr/   | England




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