Question: I have a long list of GI and I want their accession number
0
gravatar for alisa
14 months ago by
alisa0
alisa0 wrote:

Hi, As i explained before, i have a long list of GI from genebank and I want to get their corresponding accession number. Is there any way of doing this with efetch or epost? i need it to be quick.

Thank you!

myposts • 520 views
ADD COMMENTlink modified 14 months ago by Jean-Karim Heriche9.3k • written 14 months ago by alisa0

"as you explained before"? :)

ADD REPLYlink written 14 months ago by Ram11k

May be you are looking for Gene Id Conversion Tool

ADD REPLYlink written 14 months ago by venu3.5k
3
gravatar for genomax2
14 months ago by
genomax226k
United States
genomax226k wrote:

Get this file and parse out the gi/accession numbers you need: ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz

ADD COMMENTlink written 14 months ago by genomax226k

thanks. it's the file i need. 

ADD REPLYlink written 14 months ago by alisa0
1
gravatar for Jean-Karim Heriche
14 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche9.3k wrote:

Use NCBI's eutils. Something like this:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=acc&id=568815597

ADD COMMENTlink written 14 months ago by Jean-Karim Heriche9.3k
0
gravatar for Chris Miller
14 months ago by
Chris Miller18k
Washington University in St. Louis, MO
Chris Miller18k wrote:

Sounds like an ideal use case for biomart:

http://www.ensembl.org/biomart/

 

 

ADD COMMENTlink written 14 months ago by Chris Miller18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1510 users visited in the last hour