problem with remote databank access

[Jack Leunissen]

No, the problem is that their default output format is EMBL! And that seems
to upset
EMBOSS, as it expect GENBANK format for the sequence information too.

Changing the call to:
url:"http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs/wgetz?-e+-sf+g
enbank+[genbank-acc:%s]"
does the trick! (note the addition: +-sf+genbank" to force the sequence
output in GENBANK format).

Cheers,
Jack

   Jack A.M. Leunissen         Email: jackl at cmbi.kun.nl
   Centre for Molecular and    Tel  :  +31 24 365 22 48
   Biomolecular Informatics    Fax  :  +31 24 365 29 77
   Nijmegen, Netherlands       http://www.cmbi.kun.nl/


----- Original Message -----
From: "Guy Bottu" <gbottu at ben.vub.ac.be>
To: <emboss-bug at embnet.org>
Cc: <emboss at embnet.org>; <rherzog at bigben.vub.ac.be>
Sent: Friday, August 03, 2001 2:48 PM
Subject: problem with remote databank access


> from : BEN
>
> Dear support,
>
> While experimenting with remote databank access I noticed the following :
>
> DB GENBANK [ type: N format: genbank method: url
>              comment: 'GenBank at Institut Pasteur (Paris, France)'
>              url:
"http://srs.pasteur.fr/cgi-bin/srs6/wgetz?-e+[genbank-acc:%s]"
> ]
>
> does work fine. However, with :
>
> DB GENBANK [ type: N format: genbank method: url
>              comment: 'GenBank at DKFZ (Heidelberg, Germany)'
>
>
url:"http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs/wgetz?-e+[genb
ank-
> acc:%s]"
> ]
>
> seqret genbank:X15320 retrieves a file :
>
> >ECARGS X15320 Escherichia coli argS gene for arginyl-tRNA-synthetase (EC
> 6.1.1.19
>
> The problem is probably that at the DKFZ they index the databank in GCG
format.
> However, replacing "format: genbank" by "format: gcg" does not work.
>
> Guy Bottu
>
>