I am using the latest version of biomaRt (1.10.1) package with R version
2.5.1, and would like to retrieve all 3' UTR sequences in the Ensembl 46,
NCBI 36 (current versions) for the homo sapiens organism. I have used the
Vignette/documentation and tried:

> ensmart=useMart("ensembl", dataset="hsapiens_gene_ensembl")
Checking attributes and filters ... ok
> getSequence(type="ensembl", seqType="3utr", mart=ensmart)
Error in getSequence(type = "ensembl", seqType = "3utr", mart = ensmart) :
        Invalid type argument.  Use the listFilters function to select a
valid type argument.

 although both arguments to "type" and "seqType" seem to be correct, it
looks like there is something wrong with the input.

I also tried

> getSequence(type="entrezgene", seqType="3utr", mart=ensmart)

> utr3_1 = getSequence(chromosome=1, start=1, end=10000000,
type="entrezgene", seqType="3utr", mart=ensmart)
> show(utr3_1)
NULL

When I try the advanced option for retrieval, the command takes a long time
to return, and then returns the following:
> getBM(attributes=c("ensembl_gene_id","external_gene_id","3utr"),
mart=ensmart)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
:
        line 21 did not have 3 elements

I must be missing something... Any suggestions how I could get all 3' UTR
sequences for the human organism using this package?

Thank you in advance,

U.C.

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