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Question: Yeast Genome Assembly
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gravatar for Edward Turk
7.4 years ago by
Edward Turk • 100
Edward Turk • 100 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?
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modified 7.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.4 years ago by Edward Turk • 100
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gravatar for Jennifer Hillman Jackson
7.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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: http://www.yeastgenome.org/ 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, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
ADD COMMENT • link written 7.4 years ago by Jennifer Hillman Jackson ♦ 25k
Hi Jen, 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 : http://fungi.ensembl.org/Saccharomyces_cerevisiae/Info/Index]. Thank you, Edward Dr. Edward Turk, Ph.D. Postdoctoral Fellow Dep. of Molecular Biology and Microbiology Case Western Reserve University School of Medicine, Wood Bldg. W212 10900 Euclid Avenue Cleveland, OH 44106 440-487-2928 216-368-0385 edwardturk@mac.com
ADD REPLY • link written 7.4 years ago by Edward Turk • 100
Hi Edward, 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 is here: http://downloads.yeastgenome.org/genome_release/r64/ 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! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
ADD REPLY • link written 7.4 years ago by Jennifer Hillman Jackson ♦ 25k
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