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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