New & Noteworthy
March 17, 2016
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! YeastMine enables slicing and dicing of data from SGD in any way you choose. Ask questions like “Which genes can mutate to confer oxidative stress resistance, and what biological processes are they involved in?” or “Are there any undiscovered subunits of the mitochondrial ribosome?”
Take a look at our newest video tutorial to dig into YeastMine, and let us know if you have any questions or suggestions.
For more SGD Help Videos, be sure to visit our YouTube channel!
November 5, 2015
Using SGD’s Variant Viewer, you can compare the nucleotide and protein sequences of your favorite genes in twelve widely-used S. cerevisiae genomes. This tool shows alignments, similarity scores, and sequence variants for open reading frames (ORFs) from the different strains relative to the S288C reference genome. Sequence data are derived from Song et al., 2015.
Take a look at our new video tutorial to get started with the Variant Viewer, and let us know if you have questions or suggestions.
November 4, 2015
SGD’s Phenotype pages present detailed information about single mutant phenotypes for a particular gene, along with references for each observation. Phenotype pages are accessible from the ‘Phenotype’ tab of the Locus Summary and is also linked from the Mutant Phenotypes section of the Locus Summary, where the phenotype data are presented in summary form. Data are presented in tabular form on the Phenotype page.
This brief video will give you an overview of the contents and organization of SGD’s Phenotype pages.
October 29, 2015
If you’re interested in finding all the published literature about a gene or protein, there’s no need to wade through long lists of PubMed results. SGD curators have already done that for you! We review PubMed weekly for new papers about S. cerevisiae. You can find papers about a specific gene or protein on its Literature tab page (see an example).
Articles on the Literature page are categorized by several topics. The Primary Literature section lists papers in which the gene of interest is a primary focus of the study, while the Additional Literature section lists papers in which the gene is mentioned but is more peripheral to the research. There are other categories of references, and also a cool interactive graphic that shows the relationships between papers that are about the same set, or overlapping sets, of genes. You can get to the Literature page for a gene or protein via the Literature tab, located at the top of its Locus Summary page and all of its other tab pages.