We (ensembl genomes) are looking into incorporating this data but I can't promise a date yet of when it will appear in our mart
Best wishes, Paul Sent from my iPhone On 8 Feb 2012, at 21:33, Arek Kasprzyk <[email protected]> wrote: > Dear Claudio, > unless somebody else (Ensembl Genomes? I am cc'ing Paul Kersey here) is > planning to take advantage of this data, the only way that BioMart can use it > is if SGD guys set up their own BioMart server. We, of course, will be happy > to help with any technical issues should they decide to go ahead with that > but it should be their initiative > > > a > > On Wed, Feb 8, 2012 at 12:23 AM, Claudio Joazeiro <[email protected]> > wrote: > Dear Arek and Arnaud, > > I am cc'ing Rob Nash from SGD who has provided the information below > regarding how to retrieve information on yeast 3' UTRs. Is this information > sufficient or would you still need Rob and his colleagues to make their data > available through the BioMart interface? If the latter is the case, would you > mind initiating a discussion with SGD? > > Rob's comment: > > >>>"http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000129301 > Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, > Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A > (2009) Ab initio construction of a eukaryotic transcriptome by massively > parallel mRNA sequencing. > Proc Natl Acad Sci U S A 106(9):3264-9 > PMID: 19208812 > > This data was generated using RNA-seq and an algorithm to construct a > transcript catalog. > > To look at the data go to GBrowse: > > http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ > > and go to the 'Select Tracks' tab and under 'Gene Structure' click the 'All > on' box next to 'UTRs', then click on the 'Back to Browser' button at the > bottom to browse the data. > > Normally, you would be able to download the sequence from within GBrowse by > selecting the tracks, clicking the floppy disk icon and then selecting FASTA > output, but currently that feature isn't working. In the interim there is a > possible solution to this problem that a bioinformatics analyst within our > group proposed you try. Here are the steps she suggested you follow to get > the sequence: > > 1. Download the appropriate tracks from our download site in BED format > (http://www.yeastgenome.org/download-data/published-datasets-directory) > 2. Grep or otherwise filter for those entries corresponding to the 3'UTRs. > 3. Go to UCSC and click on the table browser option > (http://genome.ucsc.edu/cgi-bin/hgTables?org=human) > 4. Select clade "other", genome "S. cerevisiae" and assembly "April 2011" > 5. Upload the BED files individually by clicking "Add custom tracks" > 6. Select the output format to sequence and click on get output. > > I hope this allows you to get the UTR sequences of interest."<<< > > Thanks, > Claudio > > ________________________________________ > From: Arek Kasprzyk [[email protected]] > Sent: Tuesday, February 07, 2012 6:48 AM > To: Claudio Joazeiro > Cc: Arnaud Kerhornou; [email protected]; Paul Kersey > Subject: Re: [BioMart Users] Yeast 3'UTRs > > 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]<mailto:[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]<mailto:[email protected]>] > Sent: Thursday, February 02, 2012 3:03 AM > To: Claudio Joazeiro > Cc: [email protected]<mailto:[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<tel:%28858%29%20784-7570> > > Fax: (858) 784-9779<tel:%28858%29%20784-9779> > > > > > > > > > > > > _______________________________________________ > > Users mailing list > > [email protected]<mailto:[email protected]> > > https://lists.biomart.org/mailman/listinfo/users > > > > _______________________________________________ > Users mailing list > [email protected]<mailto:[email protected]> > https://lists.biomart.org/mailman/listinfo/users > > > > -- > > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > > > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead >
_______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
