[EMBOSS] Retrieve data from entrez
wo.granon at gmail.com
Wed Jan 26 09:47:31 UTC 2011
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.
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].
> Regards, Hans
> On 01/26/2011 09:13 AM, Wolfgang Gruber wrote:
>> 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
>> 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.
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
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