Dear Claudio, could you send me the URL of the BioMart portal you are using so i can look into it?
thank you a On Thu, Feb 2, 2012 at 12:32 AM, Claudio Joazeiro <[email protected]>wrote: > To whom it may concern: > > We are having a problem with the 3' UTR setting of the BioMart Central > Portal interface. It feels like a bug in the underlying database, so we are > hoping you would be able to diagnose/fix it. > > We need to retrieve the 3' UTRs of yeast genes. I have tried to do this in > a couple of ways: > > TRIAL 1: > > DATABASE: Ensembl > Datasets: S cerevisiae genes > Sequences: 3' UTR > Upstream Flank: (blank) > Downstream Flank (blank) > Filters: (default) > Header: Ensembl Gene ID and Associated Gene Name > > The result I got was: “Sequence unavailable” for all genes > > Then I attempted TRIAL 2: > > DATABASE: Ensembl > Datasets: S cerevisiae genes > Sequences: Flank-coding region (not ideal, though, as this is expected to > yield longer sequences than those we're looking for) > Upstream Flank: (blank) > Downstream Flank: 100 (this is also a problem because although the median > length of yeast 3' UTRs is 104 bp, they can be as long as ~1,000 bp, so we > would be missing sequences) > Filters: (default) > Header: Ensembl Gene ID and Associated Gene Name > > This works, but with the above caveats. > > Thanks in advance for your help. > > Sincerely, > > Claudio Joazeiro, Ph.D. > Assistant Professor > Department of Cell Biology > The Scripps Research Institute > CB-163 > 10550 N Torrey Pines Rd > La Jolla, CA 92037 > > Phone: (858) 784-7570 > Fax: (858) 784-9779 > > > > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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