Dear Claudio, We at BioMart do not host any data ourselves. We rely on the instances of BioMart set up by third parties. It would be probably best to ask SGD folks if they plan to make their data available through the BioMart interface in the future so those annotations could become available to the BioMart community. Failing that, perhaps Enesmbl genomes is planning to have those annotations? (I am cc'ing Paul Kersey who may want to comment on that)
a On Thu, Feb 2, 2012 at 10:02 AM, Claudio Joazeiro <[email protected]>wrote: > Dear Arnaud, > > Thank you for the prompt response. Is there interest in BioMart's part to > have yeast UTR information to provide through its portal? If so, I am > certain SGD can help since that annotation is available. I can help mediate > an introduction if you would like. > > Regarding the length of flanking sequences, I realize that I can select > any number. The problem is that yeast 3' UTRs have variable lengths so the > output for any given specified number would not be accurate for every gene. > > Regards, > Claudio > ________________________________________ > From: Arnaud Kerhornou [[email protected]] > Sent: Thursday, February 02, 2012 3:03 AM > To: Claudio Joazeiro > Cc: [email protected] > Subject: Re: [BioMart Users] Yeast 3'UTRs > > Hi Claudio, > > There is no UTR information held in Ensembl for Scerevisiae > Our data come from SGD GFF3 flat files, and I don't think they contain > UTR information. > > Re. the length of the flanking sequences, you can specify any length you > wish in the filter page. > > Regards, > Arnaud > > On 02/02/2012 05:32, Claudio Joazeiro 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 > > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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