[BioC] issue of genome build versions when using biomaRt

Al Tango time.is.flying at gmail.com
Fri Nov 7 06:53:12 CET 2008

Hi all,  Although seems a frequently asked question, I didn't find it
in archives.

When specify chromosomal coordinates for a region in using biomaRt or
other BioC packages, how can I know the version of genome assembly
being retrieved, and is it possible to define a particular version to

eg, I am searching for 5'UTR sequence of gene(s) within a region this way:

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
getSequence(chromosome=3, start=185514033, end=185535839,
type="entrezgene", seqType="5utr", mart=ensembl)

My questions: does it treat the start/end coordinates as in the latest
version of builld 36 (2006)? can I opt for build 35 or hg17 (2004)?

Thanks for your help in advance.

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