[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

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.


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