Question: I have a long list of GI and I want their accession number
0
gravatar for alisa
2.4 years 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 • 926 views
ADD COMMENTlink modified 2.4 years ago by Jean-Karim Heriche15k • written 2.4 years ago by alisa0

"as you explained before"? :)

ADD REPLYlink written 2.4 years ago by Ram15k

May be you are looking for Gene Id Conversion Tool

ADD REPLYlink written 2.4 years ago by venu5.3k
3
gravatar for genomax
2.4 years ago by
genomax50k
United States
genomax50k 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 2.4 years ago by genomax50k

thanks. it's the file i need. 

ADD REPLYlink written 2.4 years ago by alisa0
1
gravatar for Jean-Karim Heriche
2.4 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche15k 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 2.4 years ago by Jean-Karim Heriche15k
0
gravatar for Chris Miller
2.4 years ago by
Chris Miller19k
Washington University in St. Louis, MO
Chris Miller19k wrote:

Sounds like an ideal use case for biomart:

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

 

 

ADD COMMENTlink written 2.4 years ago by Chris Miller19k
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