We will add the new yeast genome from Feb 2011 to our working list of
genomes to add. (r64 dated Feb-3-2011 at SGD, dated April 2011 at NCBI).
This confirmed with SGD directly to be a more current version that the
two currently at Galaxy. The S288C_reference_genome_r64.tar.gz download
Meanwhile, the data can be loaded and added to your history and used
from there as a reference genome with most tools.
Best wishes for your project!
On 6/29/11 2:22 PM, Edward Turk wrote:
Could you update the yeast genome to match the following 2011 release?
Ensembl release 9 for Fungal database (which is dependant on SGD
database) [link :
On Jun 27, 2011, at 11:58 AM, Jennifer Jackson wrote:
> Hello Edward,
> The database Saccharomyces_cerevisiae_S288C_SGD2010 could be
> considered an update (newer release) of the SGD/sacCer2 database,
> since the source is the same - SGD:
> UCSC did not update to this newer version of the genome (yet), which
> is why in Galaxy it is not labeled with a UCSC short name (for
> example, sacCer3). If/when UCSC decides to create a sacCer3 genome
> database, we would very likely pull that over or add in the short name
> to the existing Galaxy genome (if they were the same build).
> There are advantage with deciding to use either. If using the UCSC
> genome, liftOver would be available as well as the option of viewing
> at UCSC. But using the latest genome from SGD would give you the
> highest quality assembly to work with and viewing in Trackster
> ("Visualization" at Galaxy is a great alternative.
> Hopefully this helps,
> Galaxy team
> On 6/24/11 8:40 AM, Edward Turk wrote:
>> For yeast analysis I use the following assembly: S. cerevisiae June
>> 2008 (SGD/sacCer2) (sacCer2). Recently a new yeast genome has
>> appeared as an option in Galaxy: S. cerevisae str. S288C
>> (Saccharomyces_cerevisiae_S288C_SGD2010). Is this an update to
>> sacCer2? Where is it coming from? I don't see it at UCSC?
>> The Galaxy User list should be used for the discussion of
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> Jennifer Jackson
Dr. Edward Turk, Ph.D.
Dep. of Molecular Biology and Microbiology
Case Western Reserve University
School of Medicine, Wood Bldg. W212
10900 Euclid Avenue
Cleveland, OH 44106