I am trying to DNA sequence of the upstream regulatory region of a number
of genes using the biomaRt package.  I start with a list of EntrezGene IDs
and would like to extract the sequence from 10Kb upstream of the end of the
5'UTR to the end of the 5'UTR.  I wrote a neat little package of scripts to
do this with biomaRt and export the data in .FASTA format.  I have found
that this works well when I search for one gene at a time.  But when I
input a list of entrez gene ids to the getSequence function it gives me
back sequences but the sequences do not always match the answer I get when
I search for the gene one at a time.  Sending calls to biomaRt one gene at
a time will clearly be much slower but fast searches do me little good if I
don't know whether the answer is correct or not.

The codes I have written are pretty straight forward.  The meat of the code
is the getSequence function which I call as follows:

biomart<- useMart('ensembl')
martDataset<-useDataset(
dataset,mart=biomart)
getSequence(id = '6720', type='entrezgene',seqType =
'coding_gene_flank',upstream = 10000, mart = martDataset)

As an example, when I search the 5869 gene by itself, I get the same answer
provided by the biomart web based tool.  When I search for the 5869 gene in
a list like the following list, I get a different sequence.

c('8317','1435','1063','4751','3832','3070','5869','675','81624','7249','1186','3801','672','1058','22974','23654','4171','1062','3148','4001','3007','26271','9314')


Thanks for any help with this problem.  Let me know if you need more info.
I am open to other ways of solving this problem without biomaRt
getSequence.

Thanks,
Michael Gormley

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