[BioC] issue of genome build versions when using biomaRt

Herve Pages hpages at fhcrc.org
Fri Nov 7 19:21:45 CET 2008

Hi Al,

You also have the option to retrieve those sequences from the appropriate
BSgenome data package:

  getSeq(Hsapiens, "chr3", start=185514033, end=185535839)

The hg18 genome is NCBI Build 36.1 (http://genome.ucsc.edu/FAQ/FAQreleases)


Al Tango wrote:
> 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
> use?
> 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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