[BiO BB] "The" mRNA for a gene

Amir Karger akarger at CGR.Harvard.edu
Fri Apr 20 10:00:35 EDT 2007

I'd like to get exactly one "representative" transcript (Ensembl ENST or
GenBank mRNA, say) for every gene. Due to alternative splicing and other
messy biology, Ensembl and GenBank will often have lots of mRNA's
associated with single genes. But I think it's true that for most genes,
we know of one "main" protein that that gene makes, and one isoform of
that protein will be the most studied. Swiss-PROT gives me just one mRNA
for BRCA1_HUMAN, which is nice, but for 1433E_HUMAN it gives me 7 mRNAs,
which have different lengths!

Does anyone know of a place I could get something like this? I'm happy
to do some coding if necessary. The results don't have to be perfect.
I'm just trying to do something high-throughput that gives one
believable result per gene.

- Amir Karger
Research Computing
Life Sciences Division
Harvard University

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