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
