[EMBOSS] dbigcg/dbxgcg and GCG 11

john walshaw (JIC) john.walshaw at bbsrc.ac.uk
Mon Nov 5 17:00:21 UTC 2007

Thanks Tu,

I'm having trouble with GCG databases made from EMBL-format data - have
you also got it to work with them?

Neither dbigcg nor dbxgcg produce errors when applied to GCG 11 db
files, but dbxgcg produces .pxac and .pxid files with Count = 0. dbigcg
seems to work but then seqret returns a 'seqGcgReadSeq bad ID line'.

It works ok for GCG 10 format dbs.



-----Original Message-----
From: Zheng Jin Tu [mailto:ztu at msi.umn.edu] 
Sent: 05 November 2007 16:54
To: john walshaw (JIC)
Cc: emboss at emboss.open-bio.org
Subject: Re: [EMBOSS] dbigcg/dbxgcg and GCG 11

I am using dbigcg for indexing gcgdb for emboss use

 setenv GCGDB /usr/local/db/gcgdb/current
 dbigcg -idformat genbank -directory $GCGDB/gcggenbank -filename '*.seq'
   -dbname genbank -release 160 -date 09/01/07 -outfile gb_dbigcg.log &

Thanks,  TU

On Mon, 5 Nov 2007, john walshaw (JIC) wrote:

> Hello,
> am I right in thinking that dbigcg and dbxgcg don't support GCG 11
> database formats?
> best wishes,
> Dr John Walshaw
> Department of Computational & Systems Biology
> John Innes Centre
> Norwich Research Park, Colney, Norwich NR4 7UH,   UK
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss


More information about the EMBOSS mailing list