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Indexing REBASE

Martin Hilbers mph at mph-home.dl.ac.uk
Wed Nov 12 15:19:10 EST 1997


Thure Etzold wrote:
> 
> Ray Wang wrote:
> >
> > Hello,
> >
> > I am indexing REBASE, and always meet serious segmentation Fault when
> > SRS5.05 is building the links between REBASE and SWISSPROT, REBASE and
> > SWISSNEW, REBASE and SPTREMBL, which caused core dump.
> >
> > Would anyone has an answer to solve the problem?
> 
> just in case Martin Hilbers is too busy answering on that himself.
> He has indexed Rebase on his sites and the links seem to work.
> 
> http://www.seqnet.dl.ac.uk/srs5/
> 
> ...have a look at the rebase information page and copy the Icarus
> files to your site
> 
> regards
> thure

Just one warning - I did a "dirty" trick  to create the links between
rebase
and swissprot - I linked the ID of rebase to the description field of 
swissprot, asssuming that any occurence of a word like BAMHI in that
field
indicates a protein which has something to do with that restriction
enzyme.

And the internal rebase links (ie rebase entry to rebase entry) do not
work
at the moment - got to find some time to fix that, but for the moment 
it may be better to comment that line out from the rebase.i file.

It may be worthwile to have a look at what I have called "rebcom" as
well - 
it indexes the information about restriction enzyme suppliers in
the rebase commdata.nnn file.

Cheers,

Martin

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