[EMBOSS] Antwort: genbank retrieval

[Rodrigo Lopez]

CON entries do not have sequences as described in the EMBL/NCBI/DDBJ 
guidelines. Please see:

http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.html#1_2_9

1.2.9 CON Database File

CON files include construct information for building contig sequences of 
chromosomes, genomes and other long DNA sequences. CON entries in file 
'embl.con' do not contain sequence data per se.

However, EMBL-EBI make EMBLCONEXP available. These do have the sequences 
and are available from:

ftp://ftp.ebi.ac.uk/pub/databases/embl/expanded_con/

I have not tested these with the EMBOSS dbiflat/dbxflat - but in 
principle they should work.

R:)




David.Bauer at schering.de wrote:
> 
> Hi,
> 
> I assume you mean gbcon.seq from the NCBI.
> This is a bit strange sequence database, with no sequence in it.
> It just contains instructions which part of which genbank file has to be
> used to create a non-overlapping contig.
> So this file can not be indexed with dbiflat.
> 
> David.
> emboss-bounces at emboss.open-bio.org schrieb am 03/11/2005 10:23:55:
> 
> 
>>Hi,
>>
>>I'm trying to do a retrieval (entret -EMBOSS-) of CON-division of
>>genbank database previously indexed through dbiflat but I don't obtain
>>any result.
>>Does anybody know how can I solve this problem?
>>Thank you in advance,
>>Natalia
>>_______________________________________________
>>EMBOSS mailing list
>>EMBOSS at emboss.open-bio.org
>>http://newportal.open-bio.org/mailman/listinfo/emboss
> 
> 
> 
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