New & Noteworthy
Downloads files added to YeastMine
September 20, 2023
Back in the day, SGD maintained an FTP site to distribute data in various files. More recently, you have found these files in the SGD Downloads site. We have now moved these files to YeastMine:
From the YeastMine homepage, click Templates at top left. In the Filter, select ‘Downloads’ to constrain the list of templates.
The following templates are listed under Downloads:
• Deleted Merged Features: Retrieve all deleted and merged features.
• Retrieve Functional Complementation for genes: For gene(s), retrieve information about cross-species functional complementation between yeast and another species.
• Retrieve GO Terms: Retrieve GO Terms, including name, ID, namespace, and definition.
• Retrieve SGD chromosomal Features: Retrieve genes and other chromosomal features, including IDs, coordinates, and descriptions.
• Retrieve all cross-references for all genes: Retrieve IDs for yeast gene and gene products in other databases.
• Retrieve all domains of all genes: Retrieve Proteins/Genes that have a given domain.
• Retrieve all interactions for all genes: Retrieve physical and genetic interactions for all genes.
• Retrieve all pathways for all genes: Retrieve all metabolic pathways for all genes.
• Retrieve protein properties of all proteins of ORFs: Retrieve protein properties, including pI, molecular weight, N-terminal and C-terminal sequences, codon bias, etc. of all proteins.
For help using YeastMine, please see the SGD Help Pages and YouTube Channel.
Categories: Data updates, Tutorial, Website changes
Tutorial on New SGD Features!
May 15, 2020
What are the basic features of SGD? In our new video you will learn some of the key features that are available to users to help with their research efforts.
We realize that there are many resources not included in this video (did you see that list at the end?), but we wanted to provide new users with a glimpse of some of the information they can expect to find on our detailed website.
The video is also located on our YouTube channel where we maintain other videos and tutorials regarding SGD features.
Categories: Tutorial
Explore the S288C Transcriptome in JBrowse
April 25, 2019
We have recently equipped our genome browsing tool JBrowse with 9 new Transcriptome data tracks, making JBrowse an even more powerful way to explore the vast heterogeneity of the S288C transcriptome. These information-rich data tracks visualize RNA transcripts from the TIF-seq dataset published by Pelechano et al. (2013), enabling quick and easy viewing of the position, length, and abundance of transcript isoforms sequenced in the study.
You can easily access these new tracks by entering JBrowse and clicking on the left-hand “Select tracks” tab. They are located in the Transcriptome category. In addition to viewing the data in JBrowse, you can also download the .gff3 and .bw files for these tracks for use in your own analyses.
Check out our video tutorial from the SGD YouTube channel at the top of this page for a quick overview of the new transcriptome data tracks and how to access them. More information about these tracks and how SGD created them can also be found on our Genome Browser help page.
If you have any questions or feedback about the new Transcriptome data tracks or about our genome browser, please don’t hesitate to contact us.
Data tracks that visualize transcript isoforms that fully overlap a gene coding region:
| Data Track Title | Description |
| longest_full-ORF_transcripts_ypd | This track contains the longest transcript overlapping each individual ORF completely for WT cells grown in glucose (ypd) media. |
| longest_full-ORF_transcripts_gal | This track contains the longest transcript overlapping each individual ORF completely for WT cells grown in galactose (gal) media. |
| most_abundant_full-ORF_transcripts_ypd | This track contains the most abundant transcript overlapping each individual ORF completely for WT cells grown in glucose (ypd) media. |
| most_abundant_full-ORF_transcripts_gal | This track contains the most abundant transcript overlapping each individual ORF completely for WT cells grown in galactose (gal) media. |
| unfiltered_full-ORF_transcripts | This track contains all transcripts that overlapped individual open reading frame (ORF) completely for WT cells grown in either glucose (ypd) or galactose (gal) media. |
Data tracks that quantify the number of transcripts that cover a given nucleotide in the S288c genome:
| Data Track Title | Description |
| plus_strand_coverage_ypd | For WT cells grown in glucose media (ypd), the amount of transcripts covering each position on the plus strand is represented in this track. |
| plus_strand_coverage_gal | For WT cells grown in galactose media (gal), the amount of transcripts covering each position on the plus strand is represented in this track. |
| minus_strand_coverage_ypd | For WT cells grown in glucose media (ypd), the amount of transcripts covering each position on the minus strand is represented in this track. |
| minus_strand_coverage_gal | For WT cells grown in galactose media (gal), the amount of transcripts covering each position on the minus strand is represented in this track. |
Categories: New Data, Tutorial
Sign Up Now! Next SGD Webinar: December 14, 2016
December 12, 2016
Looking for human disease-related information in SGD? There is so much to find! Active areas of curation at SGD include yeast-human homology, disease associations, alleles and phenotype variants, and functional complementation relationships.
Join our upcoming webinar on December 14th, 9:30 AM PST to learn about homology and disease data in SGD. In this quick 15 minute session, we will demonstrate the best ways to research this information on our website and provide a helpful tutorial on related SGD tools and features. Our webinars are always an excellent opportunity to connect with the SGD team–be sure to bring questions if you have them!
All are welcome to this event. If you are interested attending, please register here: http://bit.ly/SGDwebinar6
This is the sixth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.
Categories: Announcements, Homologs, Tutorial, Yeast and Human Disease
New SGD Help Video: Finding Human Homology & Disease Information
October 24, 2016
Looking for human disease-related information in SGD? There is so much to find! Active areas of curation at SGD include yeast-human homology, alleles and phenotype variants, functional complementation relationships, and disease associations. There are plenty of ways to find this information on our website, and it takes just 90 seconds to learn how – what are you waiting for?
For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!
Categories: Announcements, Homologs, Tutorial, Yeast and Human Disease
Sign Up Now for the Next SGD Webinar: September 7, 2016
September 02, 2016
The SPELL expression analysis tool at SGD makes it easy to find expression datasets and coexpressed genes that are relevant to your genes of interest. Just plug in a set of genes and go! Once given a query, SGD’s instance of SPELL locates informative expression datasets from over 270 published studies and identifies additional genes with similar expression profiles.
Find out how to use SPELL in our upcoming webinar on September 7th, 9:30 AM PDT. This quick 10-minute tutorial will explain how to run a multi-gene query in SPELL, locate expression datasets relevant to your query, and find genes with similar expression profiles.
If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar5
This is the fifth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.
Categories: Announcements, Tutorial
New SGD Help Video: Exploring Expression Datasets with SPELL
August 09, 2016
Trying to find relevant expression datasets or genes with similar expression profiles for your favorite genes? Look no further than SPELL – the Serial Pattern of Expression Levels Locator. Given a set of genes, SGD’s instance of SPELL locates informative expression datasets from over 270 published studies and pairs the genes in your query with additional coexpressed genes.
To learn the basics of SPELL and find out how to run a query, check out our help video:
For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!
Categories: Tutorial
Sign Up Now for the Next SGD Webinar: August 3, 2016
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
Next SGD Webinar: June 1, 2016
May 26, 2016
If you’re not already using JBrowse to view all your favorite S. cerevisiae genes…you should be! SGD’s JBrowse is a quick and easy way to browse through the information-rich yeast genome. Using JBrowse, you can visualize spatial relationships between genes, locate SGD annotations throughout the yeast genome, and align chromosomal features to hundreds of experimental data sets.
Our upcoming webinar on June 1st will provide a short 15-minute tutorial on the basics of JBrowse. We will demonstrate how to navigate the genome with JBrowse, locate your favorite genes or chromosomal features, and visualize experimental data with data tracks. Whether you’re an experienced GBrowse user looking to try JBrowse for the first time, or someone new to genome browsing as a whole, this webinar is sure to help you get started.
If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar3
This is the third episode of the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.
Categories: Announcements, Tutorial
New SGD Help: Downloading and Uploading JBrowse Data Tracks
May 10, 2016
SGD’s new JBrowse genome browser allows quick and easy browsing of the information-rich yeast genome.
Take a look at our newest video tutorial to learn how to download or upload JBrowse data tracks. 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: Tutorial