[EMBOSS] Retrieve data from entrez

Hans-Rudolf Hotz hrh at fmi.ch
Wed Jan 26 08:49:42 UTC 2011

Hi Wolfgang

'NP_000518' is a protein entry. You can fetch it by adding a second 
database definition (with "type: P"), ie:

DB entrezP [
          type: P
          format: genbank
          method: entrez
          fields: "id acc gi sv des org key"
          url:    "http://www.ncbi.nlm.nih.gov/sites/gquery"

and then you can fetch the protein sequence:

-bash-3.2$ seqret entrezP:NP_000518 -auto stdout |head -3
 >NP_000518 NP_000518.1 low-density lipoprotein receptor isoform 1 
precursor [Homo sapiens].

Regards, Hans

On 01/26/2011 09:13 AM, Wolfgang Gruber wrote:
> Hello,
> i am not sure if I did it the right way. I wanted to access the entrez
> database, because in general I get my sequences from there. I putted
> this entry into my emboss.default:
> DB entrez [
>           type: N
>           format: genbank
>           method: entrez
>           fields: "id acc gi sv des org key"
>           url:    "http://www.ncbi.nlm.nih.gov/sites/gquery"
> ]
> Then i tried to retrieve the data with the entrez id. In most cases
> this works, in some not. For example seqret entrez:NM_000527 works,
> but seqret entrez:NP_000518 does not: "Error: Unable to read sequence
> 'entrez:NP_000518'"
> Can you help me what I did wrong?
> Ones more what I want: I want to give the entrez id and retrieve then
> the corresponding sequence.
> Thanks,
> Wolfgang
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