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 <[email protected]>: > 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 >> _______________________________________________ >> EMBOSS mailing list >> [email protected] >> http://lists.open-bio.org/mailman/listinfo/emboss > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
