[EMBOSS] sequence retrieval

Rodrigo Lopez rls at ebi.ac.uk
Tue Jun 10 17:09:42 UTC 2008

Alternatively, look into dbfetch and wsdbfetch Web Services:



All the EMBOSS applications are available under WSDBFetch/SOAPLAB.


Peter Rice wrote:
> Jay wrote:
>> I have a large file with sequences in fasta format. They have IDs.
>> Is there any EMBOSS way to retrieve sequences by inputting a text file 
>> with
>> a short listed IDs?
> With EMBOSS you can refer to sequences in the file:
> filename:id
> You can also put a list of these into a file, and use that with
> @listfilename
> But this can be slow - it will read the file for each ID. You can also
> index the file with dbxfasta (or dbifasta) as a private database then
> define a database in your .embossrc file and use the dbname:id syntax
> (again you can use a list file, but it will be much faster)
> Hope this helps. If you need more help setting up please ask again!
> regards,
> Peter
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