[BioC] Genbank accession annotation?
James W. MacDonald
jmacdon at uw.edu
Thu Oct 3 22:34:11 CEST 2013
Hypothetically you would want to use the org.Hs.eg.db package. However,
not all GenBank assession numbers will be annotated, presumably because
they have been retired. Alternately you could use biomaRt as well.
However, the example ID you give is not annotated by either source.
On Wednesday, October 02, 2013 4:05:51 PM, Ed Siefker wrote:
> What package would I need to transform Genbank accession numbers into
> gene symbols or entrez gene ids? e.g.If I search "R28020" on NCBI, it tells
> me that "This EST is one of 1366 sequences matched to RAB2A: RAB2A,
> member RAS oncogene family. "
> Is there a metadata package that has this kind of information in it? I have a
> couple hundred such identifiers that I need to map to genes. I'd like to
> be able to run
> getSYMBOL("R28020", "some_annotation_package")
> and get a useful result. Any ideas?
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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