New & Noteworthy
2D RNA structures from RNAcentral
October 20, 2022
SGD has updated our RNA pages to add secondary structures provided by RNAcentral and generated by R2DT. Thumbnails and linkouts to RNAcentral via RNAcentral IDs are shown on the Summary and Sequence pages.
Interactive secondary structure viewers are available on the Sequence pages.
Take the pages for a spin! For more information about the structures, please see the Help page at RNAcentral.
Categories: New Data, Website changes
Tags: RNA structure
Protein Complex Page Updates
December 01, 2021
SGD has updated our protein complex pages to have the same format as gene pages, with tabs across the top for each category of information, including a Summary page, a new Gene Ontology page, and a new Literature page for each complex. Just as we do for all of your favorite genes, Gene Ontology and Literature curation for complexes will be ongoing.
If you have any questions or feedback about the updates to our complex pages, please do not hesitate to contact us at any time.
Categories: Announcements, Data updates, Website changes
Tags: protein complex, Saccharomyces cerevisiae
Explore SGD Allele Data Using New Allele Pages
October 29, 2020
We are pleased to announce that SGD’s brand new Allele Pages are now available on our website. To navigate to an allele page, use the search bar to find a specific allele or enter a gene name and select an allele from the autocomplete list. Additionally, these pages can be accessed by clicking on the allele name in a gene’s Phenotype Annotation table. These pages are still being updated with new information as it becomes available.
The type of information that you can find on each allele page includes:
- Allele Overview: General information about the allele, such as its name, the affected gene, the type of allele (e.g. missense), and a description of sequence change and/or domain mutated.
- Phenotype and Interaction Annotations: Phenotype and Genetic Interaction Annotation tables for the allele.
- Shared Alleles: A network diagram depicting shared phenotypes and interactions with other alleles.
Start browsing the thousands of alleles we now have yourself, or check out our Allele Pages video for a more detailed walk-through of what you can expect to find on each allele page:
If you are interested in viewing all alleles for a specific gene or would like to view a comprehensive list of the alleles that SGD currently has curated, you can use this YeastMine template with your customized parameters.
If you have any questions or feedback about the new Allele pages and data, please don’t hesitate to contact us at any time.
Categories: Website changes
Explore SGD with New Homepage Feature
April 06, 2020
SGD is excited to introduce the new ‘Explore SGD’ button on our homepage, which allows users to explore SGD data and pages without an initial search query.
After selecting the ‘Explore SGD’ button, users will be redirected to our search results page where they can browse all of the information SGD has to offer. The tool is designed for both new and veteran users alike, as new users are provided a glimpse into the warehouse of information SGD contains, while seasoned users may discover something new. After clicking on the ‘Explore SGD’ button, be sure to use the categories on the left to navigate through the various pages and examine areas of interest. If you are viewing this page on a mobile device, tap on “Categories” at the top of your screen to see the list of categories.
Additionally, an ‘Explore’ button has been added to the selection of links available in the black bar at the top of every page. This gives users the ability to access the search results page from anywhere on the SGD website.
Check out the new Explore features on the SGD homepage and be sure to contact us if you have any questions or feedback!
Categories: Website changes
SK1 Sequence Updated in SGD
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:
Variant Viewer will be updated in a future release. Be sure to check out these updated tools and resources and let us know if you have any questions or comments.
Categories: Data updates, Website changes
New and Improved Gene/Sequence Resources
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.
Pick up to 11 yeast strains in the new Gene/Sequence Resources
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:
- Options to select up to 11 different yeast strains for gene searches and sequence downloading
- Ability to search for multiple genes at a time
- Sequence alignment/variation tools such as Variant Viewer
- Convenient, automatic loading of your sequence/gene of interest into other tools at SGD
Be sure to check out the new and improved Gene/Sequence Resources, accessible via the Sequence section in the top purple toolbar, and let us know if you have any feedback.
Categories: Website changes
SGD: New Search, New Style
August 22, 2016
- Superior search box functionality: New autocomplete options connect to information faster than ever
- Sorting options: Results sorted alphabetically, by relevance, and by number of annotations
- Download gene lists: Export gene lists from search results into a text file with the “Wrapped” and “Download” options
- Faceted searching: Narrow search results by using categories like Genes, Molecular Functions, Phenotypes, and more!
Categories: Announcements, Website changes
Coming Soon – New Search and New Styling
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:
- an expanded selection of fields included in the autocomplete list
- the ability to enter the SGD site and explore data and pages without an initial query – just click the Explore button and go!
- narrowing of search results by categories such as genes, molecular functions, and phenotypes (and more!)
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.
Categories: Announcements, Website changes
Updated Genome Browser
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!
Categories: Data updates, Website changes
Better Performance for SGD’s Locus Summary Pages
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