February 25, 2011
In an effort to provide a comprehensive view of all of the sequence-based functional elements in the Saccharomyces cerevisiae genome, SGD will collect sequence-based functional feature annotations from published datasets, aimed at charting the yeast transcriptome (e.g. protein-coding genes, non-coding RNAs), chromatin landscapes (e.g. nucleosome phasing, histone modifications and variations), as well as cataloging regulatory sequence elements (e.g. transcription factor binding sites, splicing signals) and more.
We have upgraded our GBrowse genome viewer to allow users to quickly and easily browse this information-rich view of the yeast genome. In addition, 17 new data tracks have been added, including recent surveys of the budding yeast transcriptome (Nagalakshmi et al. 2008; Xu et al. 2009; Yassour et al. 2009) and catalogs of regions favored for recombination and replication events (Mancera et al. 2008; Buhler et al. 2007; Xu et al. 2006; Eaton et al. 2010). We invite authors to work with us to integrate their data into our GBrowse viewer pre- and/or post-publication as we move forward. Watch for the regular addition of new tracks to SGD’s GBrowse in the future! Please contact us if you are interested in participating or have questions and comments.
Categories: New Data
February 02, 2011
The budding yeast Saccharomyces cerevisiae reference genome sequence was updated today. This is the first major update of the S288C reference sequence since 1996, and 194 proteins have changed as a result of this update. The new version, called “S288C 2010”, was provided by Fred Dietrich of Duke University, and was determined using new high fidelity sequencing from an individual yeast colony. This update increases accuracy by using modern sequencing technology (Illumina HiSeq) and provides a valuable resource that will serve as the reference point from which to expand our annotation of additional S. cerevisiae strains. In the very near future, SGD will provide researchers with the genome sequences for several commonly used laboratory strains. This is a very exciting time. We will soon have the sequence of all major laboratory strains and hundreds of wild and commercial isolates. Comparative genomics with so many well-studied S. cerevisiae strains and closely-related species will enhance the awesome power of yeast genomics.