Hi Marc,

Thanks for the input.  I looked into using the GenomicRanges package but I
thought I had to generate my own TxDb and I didn't realize this would be
associated with EntrezGene IDs.  Using the already generated TxDb from
bioconductor makes this much easier.

I actually coded up my own version of this using the chromosomal locations
in the org.Hs.eg.db package and the  BSGenome library to get sequences.  I
had to fudge the identification of 5'UTRs a bit.  I used the getSeq
function to extract the entire gene sequence, searched for the first
instance of ATG and then adjusted my ranges to get the genomic region
upstream of this spot.  Obviously not as good as using annotated 5'UTRs but
good enough for my purposes.  I will implement your method for any future
projects.

Thanks again,
Mike

On Thu, Dec 15, 2011 at 6:55 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Michael,
>
> I am not actually sure how you would best do this with BiomaRt, but here
> is how you might do it using one of the TxDb packages:
>
> gids <- c('8317','1435','1063','4751',**'3832')
>
> library(TxDb.Hsapiens.UCSC.**hg19.knownGene)
> txdb <- TxDb.Hsapiens.UCSC.hg19.**knownGene
> utrs <- fiveUTRsByTranscript(txdb)
>
> ## This then gets you a GRangesList object for the entrez gene IDs in gids.
> ## This object has the ranges for the UTRs that match the different known
> transcripts for each gene.
> matches <- utrs[names(utrs) %in% gids]
> ## At this point you may decide you want more or less UTR sequence.
> ## You can easily adjust your ranges accordingly if you want something
> else.
>
> ## And once you are happy with your ranges, you can retrieve sequences
> with the help of a BSGenome package like this:
> library(BSgenome.Hsapiens.**UCSC.hg19)
> ## Then use getSeq   ( help("getSeq,BSgenome-method") )
> unlist(matches)
> seqs <- getSeq(Hsapiens, names=unlist(matches))
> ## This gives you a DNAStringSet object
> seqs
>
>
> Hope this helps,
>
>
>
>  Marc
>
>
>
>
>
> On 12/14/2011 02:14 PM, Michael Gormley wrote:
>
>> 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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>>
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