New & Noteworthy
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