November 20, 2018
The alternative reference strain SK1 is a rapid and synchronously sporulating diploid constructed by Kane and Roth in the early 1970’s to study carbohydrate metabolism under sporulation conditions. Whereas the reference strain S288C is notorious for being poor at sporulation, SK1 undergoes sporulation readily, and as such has been widely used to study the genetics of sporulation and meiosis.
The genome of SK1, which was temporarily removed from SGD, is now available once again with an updated sequence provided by Scott Keeney from the Sloan Kettering Institute. You can access the updated SK1 sequence for your favorite genes from the Sequence tab, in the Alternative Reference Strains section (example: ECM22 Sequence page). To access the entire SK1 genome sequence, visit the SK1 Strain page.
In addition, we have updated following Sequence and Analysis tools to utilize the latest SK1 sequence:
July 12, 2018
Gene/Sequence Resources (GSR) is a great way to figure out which tools at SGD can help you analyze the yeast genome. Given a gene name, chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays.
We’ve recently updated GSR to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different S. cerevisiae strains. New features in Gene/Sequence Resources include:
Categories: Website changes
August 22, 2016
August 15, 2016
SGD is planning to release a new faceted search on Monday, August 22, 2016, along with some new site styling optimized for mobile use. The refactored search has been available for the last few months on our beta site: sgd-beta.stanford.edu.
New features of the search include:
Navigating SGD will soon be easier than ever. Please explore the new search, try some different queries, view the new styling on your favorite pages, and send us your feedback via email, or through this short survey.
March 27, 2016
In an effort to provide a comprehensive view of sequence-based functional elements in Saccharomyces cerevisiae, we have upgraded our genome browser, and added new data tracks, to allow users to quickly and easily browse the information-rich yeast genome. We invite authors to work with us to integrate published data into our new JBrowse genome viewer pre- and/or post-publication. Please contact us if you are interested in participating or have questions and comments. Watch for the regular addition of new tracks to SGD’s JBrowse in the future!
Take a look at our newest video tutorial to get acquainted with JBrowse, and let us know if you have any questions or suggestions.
For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!
November 20, 2014
We heard from many of you about recent performance problems with SGD web pages, and we greatly appreciate your feedback.
The new features and new information recently added to SGD’s Locus Summary pages affected the performance of the web pages, particularly when viewed with the Google Chrome browser. We’ve been working very hard to implement solutions to address these issues. The fix is now in place and the pages now open and respond much more quickly. Please stay in touch with us as we work together to make SGD increasingly informative and useful.
Categories: Website changes
October 13, 2014
We are pleased to announce that the redesign of our gene-specific pages, which has been ongoing over the past year, is now complete with the release of the reworked Locus Summary page. The page contains all of the information on the previous Locus Summary page, and has a more modern look and feel. Note that the order and organization of the sections has changed, and the order of the tabs across the top of the page has changed as well. New elements on the page include a navigation bar on the left to take you to the different sections of the page, a redesigned map showing genomic context in the sequence section, and a new interactive histogram summarizing expression data. Biochemical pathway information now appears in its own section (see an example), and we have added a History section to replace the previous Locus History tab. If there are no data of a particular type (for example, Pathways), then that section is absent from the page.
Please explore this new page and send us your feedback.
October 06, 2014
The Expression pages have been redesigned and now include a clickable histogram depicting conditions and datasets in which the gene of interest is up- or down-regulated. Expression data are derived from records contained in the Gene Expression Omnibus, and datasets are assigned one or more categories to facilitate grouping, filtering and browsing. Short descriptions of the focus of each experiment are also provided. The PCL files generated for each dataset are used to populate the expression analysis tool SPELL. Also included on the pages are network diagrams which display genes that share expression profiles. The Expression pages provide seamless access to the SPELL tool at SGD, as well as external resources such as Cyclebase, GermOnline, YMGV and FuncBase.
Please explore these new pages, accessible via the Expression tab on your favorite Locus Summary page, and send us your feedback.
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.
June 24, 2014
We have redesigned the Protein page to include a new tabular display of protein domains. This table provides the identifier for each domain and illustrates the respective locations of the domains within the protein. In addition to this new table, the domains are displayed in an interactive network diagram that presents the proteins that share these domains with your protein of interest (see figure below, left).
Another new feature on the Protein page is the display of phosphorylation sites within the protein’s sequence (as curated by BioGRID). This feature is available for both the reference strain S288C and other commonly used S. cerevisae strains, using the pull-down to select the desired strain view (see figure below, right) .