New & Noteworthy

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.

gsr-strains

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


SGD is pleased to introduce our new faceted search, replete with new features that make navigating SGD easier than ever. It’s simple to get started – just click on the “Try this?” button on the SGD homepage. Try a search for your favorite gene or your favorite topic of study in our improved search box! We have also introduced a sleek new look that retains the same familiar features and menus, but is now optimized for mobile use.
 
New features of the search include:
  • 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!
To get familiar with the new search, check out this quick help video to get started:
 

As you explore SGD’s new and improved search, please be sure to send us any feedback via email or through this short survey.
 

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

New and improved Locus Summary pages

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.

Categories: New Data, Website changes

Redesigned Expression pages

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.

Categories: New Data, Website changes

New Sequence, Chromosome, and Contig pages

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: Website changes, New Data, Data updates, Sequence

Shared Domains and Phosphorylation Sites on Protein Pages

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) .

Left: Proteins (gray circles) that share domains (colored squares) with Fas1p (yellow circle). Right: an example of some of the phosphorylation sites in Swe1p (red residues).

Proteins that share domains with Fas1p

Swe1p protein sequence and phophorylation sites highlighted in red.

Categories: New Data, Website changes

Educational Resources on the SGD Community Wiki

February 21, 2014

Did you know you can find and contribute teaching and other educational resources to SGD? We have updated our Educational Resources page, found on the SGD Community Wiki. There are links to teaching resources such as classroom materials, courses, and fun sites, as well as pointers to books, dedicated learning sites, and tutorials that can help you learn more about basic genetics. Many thanks to Dr. Erin Strome and Dr. Bethany Bowling of Northern Kentucky University for being the first to contribute to this updated site by providing a series of Bioinformatics Project Modules designed to introduce undergraduates to using SGD and other bioinformatics resources.

We would like to encourage others to contribute additional teaching or general educational resources to this page. To do so, just request a wiki account by contacting us at the SGD Help desk – you will then be able to edit the SGD Community Wiki. If you prefer, we would also be happy to assist you directly with these edits.

Note that there are many other types of information you can add to the SGD Community Wiki, including information about your favorite genes, protocols, upcoming meetings, and job postings. The Community Wiki can be accessed from most SGD pages by clicking on “Community” on the main menu bar and selecting “Wiki.” The Educational Resources page is linked from the left menu bar under “Resources” from all the SGD Community Wiki pages. For more information on this newly updated page, please view the video below, “Educational Resources on the SGD Community Wiki.”

Categories: New Data, Website changes

Tags: teaching, educational, Saccharomyces cerevisiae, genetics

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