[EMBOSS] Antwort: dbifasta and ncbi formats

[David.Bauer at SCHERING.DE]

Hi,

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 are
also ignored.
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:
http://emboss.sourceforge.net/docs/adminguide/node4.html#SECTION00422150000000000000


Hope this helps,
David.

emboss-bounces at emboss.open-bio.org schrieb am 23/10/2005 19:29:07:

> Hi,
>
>
>
> Sorry for trivial question. What are available „formats” for ncbi fastA
> format ?
>
>
> ncbi
>
> (| formats)
>
>
>
> I don’t figure out, how to specify these (| formats)
>
>
>
> If I run dbifasta and choose –idformat ncbi  then after creating
database
> index seqret returns sequences only when I specify NP_414542.1 and not
by gi
> number.  How can I use the gi number for retrival as well?
>
>
>
> Example header of FastA flatfile
>
>
>
> >gi|16127995|ref|NP_414542.1|     thr operon leader peptide [Escherichia
> coli K12]
>
>
>
> AND
>
>
>
> Database definition is here
>
>
>
> DB ec [
>
>    type: P
>
>    dir: /home/db/coli
>
>    method: emblcd
>
>    format: fasta
>
>    file:ecoli_p.faa
>
>    comment: "E.coli proteom from NCBI"
>
> ]
>
>
>
>
>
> Thanks
>
> Tonu
>
>
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