Alternatively, look into dbfetch and wsdbfetch Web Services:
http://www.ebi.ac.uk/dbfetch
http://www.ebi.ac.uk/Tools/webservices
All the EMBOSS applications are available under WSDBFetch/SOAPLAB.
R:)
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
_______________________________________________
EMBOSS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/emboss
_______________________________________________
EMBOSS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/emboss
