New & Noteworthy
SGD Help Video: Gene Name Reservation
July 13, 2015
The eminent Drosophila geneticist Michael Ashburner famously said: “Biologists would rather share their toothbrush than share a gene name.” It’s true that assigning names to genes is often a sticky subject.
In the Saccharomyces cerevisiae community we’re very lucky to have well-defined guidelines for genetic nomenclature, an established system for reserving gene names, and criteria for making them “standard,” or official, names. This system was agreed upon by yeast researchers nearly two decades ago and has served the community well.
Take a look at this video to get an overview of how the gene naming system works. And as always, please contact us with any questions or suggestions.
Categories: Tutorial
Tags: gene nomenclature, Saccharomyces cerevisiae, video
SGD Help Video: YeastMine is Awesome!
July 07, 2015
If you’re not already using YeastMine to answer all your questions about the Saccharomyces cerevisiae genome and the gene products it encodes…you should be!
This versatile tool lets you slice and dice data from SGD in any way you choose. You can ask questions like “How many proteins between 25 and 35 kDa in size are integral to the nuclear membrane?” or “Which genes can mutate to confer oxidative stress resistance, and what biological processes are they involved in?”
Start with this video to see a quick sample of three cool features in YeastMine.
Categories: Tutorial
New SGD Help Video: Yeast-Human Functional Complementation Data
June 30, 2015
Yeast and humans diverged about a billion years ago, but there’s still enough functional conservation between some pairs of yeast and human genes that they can be substituted for each other. How cool is that?! Which genes are they? What do they do?
This two-minute video explains how to find, search, and download the yeast-human functional complementation data in SGD. You can find help with many other aspects of SGD in the tutorial videos on our YouTube channel. And as always, please be sure to contact us with any questions or suggestions.
Categories: Homologs, New Data, Tutorial
Tags: video, yeast model for human disease
New fungal homolog data at SGD
September 15, 2014
Have you ever wondered about the role played by the homolog of a particular yeast gene in other fungal species? SGD’s advanced search tool, YeastMine, can now be used to find homologs of your favorite Saccharomyces cerevisiae genes in the pathogenic yeast, Candida glabrata. There are now 25 species of pathogenic and non-pathogenic fungi in YeastMine, including S. cerevisiae.
The fungal homologs of a given S. cerevisiae gene can be found using the template called “Gene –> Fungal Homologs.” Fungal homology data comes from various sources including FungiDB, the Candida Gene Order Browser (CGOB), the Yeast Gene Order Browser (YGOB), the Candida Genome Database (CGD), the Aspergillus Genome Database (AspGD) and PomBase, and the results link directly to the corresponding homolog gene pages in the relevant databases.
A results table is generated after each query and the identifiers and standard names for the fungal homologs are listed in the table. As with other YeastMine templates, results can be saved as lists for further analysis. You can also create a list of yeast gene names and/or identifiers using the updated Create Lists feature that allows you to specify the organism representing the genes in your list. The query for homologs can then be made against the custom gene list.
All of the new templates that query fungal homolog data can be found on the YeastMine Home page under the “Homology” tab. This template complements the template “Gene → Non-Fungal and S. cerevisiae Homologs” that retrieves homologs of S. cerevisiae genes in humans, rats, mice, worms, flies, mosquitos, and zebrafish.
We invite you to watch SGD’s YeastMine Fungal Homologs video tutorial (also available below) for tips on accessing Fungal Homolog data at SGD. You can view all Video Tutorials for YeastMine here.
Categories: Homologs, New Data, Tutorial
Create, Analyze, Save: the Power of Gene Lists in YeastMine
May 30, 2014
If you love to make and analyze lists of genes, you will love YeastMine – you can use it to create all kinds of lists! For instance, use a YeastMine template to search for all genes associated with a given GO term or phenotype observable and save these genes as a list. Or, search for all genes that interact with your gene of interest and save that as a gene list.
What’s even more fun is that you can make lists from your lists! For instance, take the list of genes you found to be associated with a given GO term and plug it into a YeastMine query template to find all the genes that interact with your list of genes – then save those genes as a list. The possibilities are endless given the different types of queries you can perform using YeastMine! Who knows what biological connections you will uncover?
Lastly, save your lists for future use by creating a MyMine account – all you need to sign up is an email and a password.
You can find a link to YeastMine in the top right corner of most SGD pages (“YeastMine: Batch Analysis or Advanced Search”) or go to SGD’s purple main menu bar, click on “Analyze” and select “Gene Lists” to go straight to creating a List in YeastMine.
To see how simple it is to save your search results as a List in YeastMine, view this brief tutorial – YeastMine: Saving Search Results as a List. To view other great SGD tutorials, YeastMine and otherwise, visit and “Subscribe” to the Saccharomyces Genome Database Channel on YouTube.
Categories: Tutorial
SGD: New look, new features!
January 26, 2012
SGD has added more than just a new look, we’ve added some great new features!
View the short video “We’ve added more than just a new look…” on Vimeo to learn about our enhanced Search Box and our new navigational menu bar.
Categories: Tutorial, Website changes
New data tracks added to GBrowse
January 26, 2012
SGD has added a mélange of data tracks to our GBrowse genome viewer from six publications covering various applications of high-throughput sequencing, including genome-wide distributions of DNase I-protected genomic footprints (Hesselberth et al. 2009), recombination-associated double strand breakpoints (Pan et al. 2011), polyadenylation sites (Ozsolak et al. 2010), antisense ncRNAs (Yassour et al. 2010), cryptic unstable transcripts (CUTs) (Neil et al. 2009) and Xrn1-sensitive unstable transcripts (XUTs) (van Dijk et al. 2011). You can now also easily download data tracks, metadata and supplementary data by clicking on the ‘?’ icon on each data track within GBrowse. Please watch our video tutorial for more information on how to download data from GBrowse. We welcome new data submissions pre- or post-publication and invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers. Please contact us if you are interested in participating or have questions and comments. Happy browsing!
View Downloading GBrowse Data at SGD on Vimeo.
Categories: New Data, Tutorial
YEASTBOOK now available!
November 15, 2011
YEASTBOOK is now available in the November 2011 issue of GENETICS. This month’s issue includes a Perspectives article by David Botstein and Gerry Fink, a review about transcriptional regulation written by Steve Hahn and Elton Young, and a review about sporulation written by Aaron Neiman. Edited by Alan G. Hinnebusch, YEASTBOOK will be a compendium of comprehensive reviews that provides the current state of knowledge of the molecular biology, cellular biology, and genetics of Saccharomyces cerevisiae. Approximately 50 YEASTBOOK review articles will be published in GENETICS (a peer-edited journal of the Genetics Society of America) over the next two years. Gene names mentioned in YEASTBOOK reviews are linked back to SGD.
Read an editorial by Alan Hinnebusch and Mark Johnston to find out more about YEASTBOOK.
Categories: Tutorial
Short Video Tutorials for Using SGD Tools
September 20, 2011
SGD is developing a library of short video tutorials designed to step you through using various SGD tools. Check out those currently available for YeastMine, GBrowse, and SPELL, located on our SGD Video Tutorials page. Preview the “YeastMine is Awesome” video below, describing just a few of the “awesome” things you can do in YeastMine!
Categories: Tutorial