problems building Genbank (GCG)

"J.A.C. Rullmann", Ton j.rullmann at organon.oss.akzonobel.nl
Fri Feb 27 03:12:10 EST 1998


As a newcomer to SRS I ran into problems building the indices for
GenBank (GCG format).
I'm using SRS 5.1.0 on IRIX 6.4. The GenBank release is 104 (12/97), as
obtained from GCG.

I tried to modify genbank.i to switch from EMBL to GCG format.
srsbuild -info genbank seems to work fine.
srsbuild -w genbank gives the following:

> ...processing GENBANK
> ...processing /u04/gcggenbank/gb_ba.ref
> ...processing /u04/gcggenbank/gb_ba.seq
> Entry name mismatch:  ref=A16SRRNA, seq=
>
But I can't see anything wrong with the file headers:

> % head /u04/gcggenbank/gb_ba.ref
> >>>>A16SRRNA  7/97
> X87617 Actinomycete (genus unknown) 16S ribosomal RNA. 7/97
>
> ....
>
> % head /u04/gcggenbank/gb_ba.seq
> >>>>A16SRRNA  7/97  2BIT  Len: 1497
> X87617 Actinomycete (genus unknown) 16S ribosomal RNA. 7/97
>

This problem did not occur when building the SwissProt indices.

Any suggestions? Thanks!

Ton Rullmann
MDI-RIM group, Organon, the Netherlands






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