July 28, 2016
SGD’s Variant Viewer is an easy-to-learn web application that allows visualization of differences in both gene and protein sequences. With Variant Viewer, you can compare the nucleotide and amino acid sequences of your favorite genes in twelve widely-used S. cerevisiae strains. Our upcoming webinar on August 3rd, 9:30 AM PDT will provide a quick 10 minute tutorial on how to use Variant Viewer. We will demonstrate how to compare nucleotide and amino acid sequences of different S. cerevisiae genomes, and how to visualize strain-specific single nucleotide polymorphisms, insertions, and deletions contained within a given open reading frame.
If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar4
This is the fourth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.
Categories: Announcements, Sequence, Tutorial
November 05, 2015
Using SGD’s Variant Viewer, you can compare the nucleotide and protein sequences of your favorite genes in twelve widely-used S. cerevisiae genomes. This tool shows alignments, similarity scores, and sequence variants for open reading frames (ORFs) from the different strains relative to the S288C reference genome. Sequence data are derived from Song et al., 2015.
Take a look at our new video tutorial to get started with the Variant Viewer, and let us know if you have questions or suggestions.
Categories: Sequence, Tutorial
February 23, 2015
SGD curators periodically update the chromosomal annotations of the S. cerevisiae Reference Genome, which is derived from strain S288C. Last November, the genome annotation was updated for the first time since the release of the major S288C resequencing update in February 2011. Note that the underlying sequence of 16 assembled nuclear chromosomes, plus the mitochondrial genome, remained unchanged in annotation release R64.2.1 (relative to genome sequence release R64.1.1).
The R64.2.1 annotation release included various updates and additions. The annotations of 2 existing proteins changed (GRX3/YDR098C and HOP2/YGL033W), and 1 new ORF (RDT1/YCL054W-A) and 4 RNAs (RME2, RME3, IRT1, ZOD1) were added to the genome annotation. Other additions include 8 nuclear matrix attachment sites, and 8 mitochondrial origins of replication. The coordinates of many autonomously replicating sequences (ARS) were updated, and many new ARS consensus sequences were added. Complete details can be found in the Summary of Chromosome Sequence and Annotation Updates.
Categories: Data updates, New Data, Sequence
December 08, 2014
At SGD, we are expanding our scope to provide annotation and comparative analyses of all major budding yeast strains, and are making progress in our move toward providing multiple reference genomes. To this end, the following new S. cerevisiae genomes have been incorporated into SGD as “Alternative References”: CEN.PK, D273-10B, FL100, JK9-3d, RM11-1a, SEY6210, SK1, Sigma1278b, W303, X2180-1A, Y55. These genomes are accessible via Sequence, Strain, and Contig pages, and are the genomes for which we have curated the most phenotype data, and for which we aim to curate specific functional information. It is important to emphasize that we are not abandoning a standard sequence; S288C is still in place as “The Reference Genome”. However, we do recognize that it is helpful for students and researchers to be able to ‘shift the reference’, selecting the genome that is most appropriate and informative for a specific area of study.
These new genome sequences have been also been added to SGD’s BLAST datasets, multiple sequence alignments, the Pattern Matching tool, and the Downloads site. Please explore these new genomes, and send us your feedback.
Categories: Data updates, New Data, Sequence
Tags: reference genome, Saccharomyces cerevisiae, strains
August 25, 2014
New Sequence pages are now available in SGD for virtually every yeast gene (e.g., HMRA1 Sequence page), and include genomic sequence annotations for the Reference Strain S288C, as well as several Alternative Reference Genomes from strains such as CEN.PK, RM11-1a, Sigma1278b, and W303 (more Alternative References coming soon). Each page includes an Overview section containing descriptive information, maps depicting genomic context in Reference Strain S288C (as shown below) and Alternative Reference strains, as well as chromosomal and relative coordinates in S288C.
The sequence itself includes display options for genomic DNA, coding DNA, or translated protein.
Also available on each Sequence page are links to redesigned S288C Chromosome pages, links to new Contig pages for Alternative Reference Genomes, and a Downloads menu for easy access to DNA sequences of several other industrial strains and environmental isolates. The new Sequence, Chromosome, and Contig pages make use of many of the features you enjoy on other new or redesigned pages at SGD, including graphical display of data, sortable tables, and responsive visualizations. The Sequence pages also provide seamless access to other tools at SGD such as BLAST and Web Primer. Please explore these new pages, accessible via the Sequence tab on your favorite Locus Summary page, and send us your feedback.
Categories: Data updates, New Data, Sequence, Website changes
December 12, 2012
SGD has incorporated two new S. cerevisiae strain genomes: CEN.PK113-7D and ZTW1. CEN.PK113-7D is a laboratory strain derived from parental strains ENY.WA-1A and MC996A, and is popular for use in systems biology studies. ZTW1 was isolated from corn mash used for industrial bioethanol production in China in 2007. We have also incorporated an updated genomic sequence for W303-derivative K6001, a key model organism for research into aging. The previous version of W303 was an early view courtesy of Markus Ralser. SGD has updated the ORF DNA and protein sequence alignments to include these two additional strains, and the updated W303. We have also included the new genomic, coding, and protein sequences in both the BLAST Search and Pattern Matching (PatMatch) tools. The alignments are accessible via the Analyze Sequence section on the Locus Summary pages. Also available are retrieval and download options.
October 03, 2011
SGD now has available ORF DNA and protein sequence alignments for dozens of S. cerevisiae strains. The alignments are accessible via a new ‘Analyze Sequence’ section on the Locus Summary pages. Also available are retrieval and download options. Stay tuned in the coming months as SGD continues to develop additional tools for viewing and analysis of these sequences.
September 06, 2011
SGD has updated both its BLAST Search and Pattern Matching (PatMatch) tools to include genomic, coding, and protein sequences from 26 additional S. cerevisiae strains. Look for more updates and tools from SGD for analyses of the S. cerevisiae strain genomes in the coming months.
Categories: Sequence, Website changes
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.
Categories: New Data, Sequence