[BiO BB] Translate Ensembl Transcript ID to NCBI GB or gi IDs?

Maximilian Haeussler maximilianh at gmail.com
Tue Mar 28 11:18:43 EST 2006

I don't know much about ensembl and their tables. but ucsc is linking
its known genes to both ensembl and ncbi refseqs.
This is part of the output of the table browser:
Database: hg17    Primary Table: knownGene    Row Count: 39,368
Description: Protein coding genes based on proteins from SWISS-PROT,
TrEMBL, and TrEMBL-NEW and their corresponding mRNAs from GenBank
hg17.knownToEnsembl.name (via knownGene.name)
hg17.knownToLocusLink.name (via knownGene.name)
hg17.knownToPfam.name (via knownGene.name)
hg17.knownToRefSeq.name (via knownGene.name)

I guess you can connect to their mysql server and generate a table to
translate your ids...

Hope that helped,

On 16/03/06, Amir Karger <akarger at cgr.harvard.edu> wrote:
> I'm blasting a bunch of sequences against the Ensembl CDNA Human Genome,
> which provides Ensemble Transcript IDs (e.g., ENST00000326632). Is there an
> easy way to convert those to GenBank identifiers or GIs? BioMart offers to
> give all kinds of IDs, but NCBI IDs don't seem to be in the list. And I was
> unable to find translation files in some digging at the NCBI and Ensembl web
> sites.
> I'm happy to do it with a script, if there's a conversion file available. An
> online resource is OK, too, of course. Is the information found in the
> Ensembl MySQL stuff somewhere, such that I could get it with the Perl API?
> Thanks,
> - Amir Karger
> Computational Biology Group
> Bauer Center for Genomics Research
> Harvard University
> 617-496-0626
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
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Maximilian Haeussler,
CNRS Gif-sur-Yvette, Paris
tel: +33 6 12 82 76 16
icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
skype: maximilianhaeussler

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