problems building Genbank (GCG)

Martin Hilbers mph at dl.ac.uk
Fri Feb 27 04:52:10 EST 1998


J.A.C. Rullmann, Ton wrote:
> 
> 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=
> >
> 

I've seen this also and the fix was changing the line

('ORIGIN' {$Not} lnT {$App})+ lnT)?

to

('ORIGIN' {$Not} lnT {$App})+ lnT lnT?)?

in the entry production in genbank.is. Check
http://www.seqnet.dl.ac.uk/srs5bin/cgi-bin/wgetz?-fun+PageIcarusFile+-l+GENBANK+-ifile+is
for a genbank.is which works with gcg genbank. It also handles the
citation field, and does the hyperlinks in the db_xref fields in
the feature tables correctly.

Cheers,

Martin

PS - release 104 ??? - the latest release is 105 !
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