NCBI query: how to find gid from locus?

Question

[weiduan93]

Hi guys, I'm currently have a buntch of locus information(with prefix NM_) and I want retrieve their sequence information from NCBI. As far as I know NCBI's api (like Biopython.Entrez) only support queries by gid,and I did a lot of searches but found no solution of getting to know a gid from its locus. Could anyone help me with this?

[Prasad]

If you are using linux machine

for i in `cat id_file`; do curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=$i&retmode=text&rettype=fasta" >>out.fasta; done;

[weiduan93]

Thanks everyone! I was soooooooo stupid that I thought the 'id' parameter of Biopython.Entrez.efetch should be passed as the gid only, but just now I tried the locus ID and succeeded TUT

Answer 1

[Sej Modha]

Have you tried NCBI e-utils?

Answer 2

[Jenez]

Just so you know; NCBI are phasing out the usage of GI's in September.

http://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/

Use Accession.Version instead.