[BiO BB] ncbi entry retrieval
Siddhartha Basu
basu at pharm.sunysb.edu
Mon Sep 18 16:35:50 EDT 2006
divyaps at ncbs.res.in wrote:
> dear all,
> I was doing a psiblast search with the organism specific peptide
> sequence downloaded from ensembl.Now I have the blast output
> sequences with ensemble id. I need to retrieve the corresponding ncbi
> entries of these psiblast hits. Is there any way to do the same? A
> software, server or a perl script? A suggestion or solution will be highly
> appreciated.
>
> thanks in advance
>
> divya p syamala
> NCBS
>
Hi,
Presuming that you are looking to convert your ensembl ids to entrez
ids, biomart (http://www.ensembl.org/Multi/martview) should be a good
option. In the first screen, choose your organism, in the second load
your ensembl ids(in the id list limit) and in the third, select out
"EntrezGene ID" in the "External References" section. Lastly, select the
output format you prefer and click export. Hopefully, that will do the
conversion for you.
-siddhartha
>
>
>
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