[Bioc-devel] how to get genomic sequences?

Sean Davis sdavis2 at mail.nih.gov
Wed Mar 28 03:28:20 CEST 2007

Sean Davis wrote:
> 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:
> http://genome.ucsc.edu/cgi-bin/das/hg18/dna?segment=chr1:1000,2000;segment=chr2:1000,2000
> 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.

Just a quick followup and a skeleton function...  The function takes a 
dataframe with three columns, chrom, start, end and a single character 
argument, genome, which needs to match the UCSC genome browser notation 
for the genome build.  It fetches the das DNA one at a time and returns 
the original dataframe and a fourth column with the sequence.  There 
isn't any error checking, etc., and it fetches one sequence at a time.  
Both of these issues could be eliminated with a little work.

getSequences <- function(locs,genome='hg18') {
  chrom <- locs$chrom
  starts <- locs$start
  ends <- locs$end
  seqs <- vector('character',length=length(chrom))
  for(i in 1:length(chrom)) {
    url <- 
    results <- xmlRoot(xmlTreeParse(url))
    seqs[i] <- gsub('\n','',xmlValue(results[[1]][[1]]))

And you could use it like so:

mySeqs <- 

Herve Page's solution is undoubtedly the better one, but if memory is a 
limitation, this solution might be of use.


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