[EMBOSS] Antwort: Retrieve data from entrez

david.bauer at bayer.com david.bauer at bayer.com
Wed Jan 26 08:39:28 UTC 2011


the entrez method looks at the type (N or P) to formulate the eutils 
request to the ncbi server.
As NP_ is a protein sequence, the database specified in the request must 
be protein and not nucleotide.
So you need two separate entries in emboss.default for nucleotide and 
protein sequences.


emboss-bounces at lists.open-bio.org schrieb am 26/01/2011 09:13:27:

> 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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