[Bioc-devel] how to get genomic sequences?

Sean Davis sdavis2 at mail.nih.gov
Wed Mar 28 01:07:12 CEST 2007

Roger Liu wrote:
> Hi,
> I have a set of data with chromosome number and coordinates of the sequences
> such as,chr10, start 1000, end 2000.
> I have tried using biomart to retrieve the genomic sequences for my dataset,
> but I didn't get success, I used seqType argument as:
> seqType="genomic", it reported error as"The type of sequence specified with
> seqType is not available. Please select from: cdna, peptide, 3utr, 5utr",
> but I have seen this "genomic" argument for seqType in the help file. So
> what's going on there?
> Or anyone can recommend a package which can help me retrieve the genomic
> sequences from hg18 with known chromosome number and sequences
> coordinates(start and end).
URLs like so:


will get you sequences of interest.  These come as simple well-formed 
XML, so you can use the XML package to parse them pretty easily.  You 
can do one-at-a-time, or string together a bunch.


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