[EMBOSS] Antwort: dbifasta and ncbi formats

Allen Smith easmith at beatrice.rutgers.edu
Mon Oct 24 06:47:55 UTC 2005

In message
<OFCDC6D3D5.1AA8D675-ONC12570A4.00205F55-C12570A4.0022C871 at schering.net> (on
24 October 2005 08:19:55 +0200), David.Bauer at SCHERING.DE
(David.Bauer at SCHERING.DE) wrote:
>the ncbi format is not fully supported by emboss. So you can only retrieve
>by the first acc (with version), not with gi and in case of nr (several
>entries separated by Ctrl-A) the other accs arealso ignored.

Ah. That answers my earlier question.

>You can format the ncbi fasta file with formatdb -o T and then specify
>fastacmd as app in emboss. In the adminguide is a short description about
>external access methods:

Would using dbiblast be an alternative? What are its capacity limits? I had
to use dbxfasta, not dbifasta on the nr database due to size - would the
same be true for dbiblast (and there isn't a dbxblast, I see...)?



Allen Smith                       http://cesario.rutgers.edu/easmith/
February 1, 2003                               Space Shuttle Columbia
Ad Astra Per Aspera                     To The Stars Through Asperity

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