transfac accession query off by one

Peter Rice pmr at sanger.ac.uk
Tue Jun 25 03:56:10 EST 1996


In article <4qnehs$1nn at usenet.ucs.indiana.edu> gilbertd at sunflower.bio.indiana.edu (Don Gilbert) writes:
>   i tried installing transfac data into srs4 today, and
>   found that accession number queries are off by one
>   (query for R02509 returns R02508) and the acc num isn't listed
>   in the report.  this is using default transfac.sdl, and
>   fiddling w/ that sdl didn't cure anything.  same problems
>   shows up at srs/ebi & srs/sanger.

Oops. Thought I had caught those ones. Nope, I did it for RHDB and friends
though.

The problem seems to be databases like TFSITE (in this case) where the
flat file has the accession number *before* the ID. This seems to mean that
when the "AC   RH02509" line is reached, the parser still thinks it is
on the previous entry.

The fix is probably to make the "AC" line the ID for the entry, and
do something else with the ID line for now (I used "DF_NAM" for RHMAP).
This makes the accession number show up as the entry name.

Our transfac.sdl file has this change now, and seems to be OK on a
quick test.

No doubt fixed in SRS 5, but for now we have to work around as far as
I can see.
--
------------------------------------------------------------------------
Peter Rice                           | Informatics Division,
E-mail: pmr at sanger.ac.uk             | The Sanger Centre,
Tel: (44) 1223 494967                | Wellcome Trust Genome Campus,
Fax: (44) 1223 494919                | Hinxton, Cambs, CB10 1SA,
URL: http://www.sanger.ac.uk/~pmr/   | England




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