secondary accession numbers
Reinhard Doelz
doelz at comp.bioz.unibas.ch
Fri Jul 2 00:52:06 EST 1993
In article <1993Jul1.234108.1 at molbiol.ox.ac.uk>, rhubner at molbiol.ox.ac.uk writes:
...
|> may represent *secondary* accession numbers and can not be searched for by
|> FETCH (and especially STRINGSEARCH; only ref fields) in GCG. This was the
^^^
DE
The problem which is described by you applies only to those secondary
accession numbers which occur more than once.
The accession numbers are used as identifiers in GCG. Look at the .numbers
file and see
biox > more /bioy/data/xembl/xembl.numbers
D00410 10824 S
D00515 9593 S
D00683 3219 S
D00684 3219 S
D00739 11834 S
D00819 10077 P
D00821 11584 S
D00844 3136 P
D00849 3049 S
D01022 6221 P
...
'S' for secondary and 'P' for primary.
If the secondary accession number occurs only *once* then GCG will work
due the fact that it is unique.
In your case,
/bioy/data/gcgembl/em_pr.ref:AC M18693; J03516; M18691;
/bioy/data/gcgembl/em_pr.ref:AC M18694; J03516; M18691;
/bioy/data/gcgembl/em_pr.ref:AC M18695; J03516; M18691;
/bioy/data/gcgembl/em_pr.ref:AC M18696; J03516; M18691;
/bioy/data/gcgembl/em_pr.ref:AC M18697; J03516; M18691;
/bioy/data/gcgembl/em_pr.ref:AC M18698; J03516; M18691;
/bioy/data/gcgembl/em_pr.ref:AC M18699; J03516; M18691;
/bioy/data/gcgembl/em_pr.ref:AC M18700; J03516; M18691;
/bioy/data/gcgembl/em_pr.ref:AC M18692; J03516;
we can see that J03516 occurs more than once.
Followups redirected to bionet.software.gcg.
> The SRS software can do the job properly...
I work with SRS, and can recommend the software for these purposes.
Thure Etzold made the code available without cost and I appreciate this
very much. The indices for the full set of sequence databases (PIR,
SWISSPROT, EMBL, GENBANK exclusion) occupy only about 130 MByte disk
space which is relatively little as compared to 500 MByte of data.
Regards
Reinhard
--
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| Dr. Reinhard Doelz | RFC doelz at urz.unibas.ch |
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