[EMBOSS] Retrieve data from entrez

[Wolfgang Gruber]

I understand. Thank you very much! I didn't recognize the type switch.

In general: Is this way ok to get the Sequences behind an entrez id?
Or is there a more specific way? Because this way I can also specify a
search term and then I get more than one result.

Thanks,
Wolfgang


2011/1/26 Hans-Rudolf Hotz <hrh at fmi.ch>:
> 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].
> mgpwgwklrwtvalllaaagtavgdrcernefqcqdgkcisykwvcdgsaecqdgsdesq
> etclsvtcksgdfscggrvnrcipqfwrcdgqvdcdngsdeqgcppktcsqdefrchdgk
> -bash-3.2$
>
>
> 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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>