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

Amir Karger akarger at CGR.Harvard.edu
Thu Mar 16 09:56:00 EST 2006

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

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?


- Amir Karger
Computational Biology Group
Bauer Center for Genomics Research
Harvard University

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