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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