New & Noteworthy
Predicted 3D Structures of Yeast Complexes
January 20, 2022
In an exciting new paper, Humphreys et al. describe the use of deep-learning-based algorithms to predict structures of not only single proteins, but assemblies of proteins. The team used rapid RoseTTAFold combined with the more accurate AlphaFold to build structural models for 106 previously unidentified protein assemblies and 806 complexes that had not been structurally characterized. The complexes have up to five subunits and are involved in numerous critical roles in cell biology.
Go look for your own proteins of interest at the ModelArchive and search in the Home page. Also find the link on the resources section of the SGD Interaction and Protein pages.
Categories: Announcements, Data updates, Paper of the Week
Tags: protein complex, Saccharomyces cerevisiae, yeast protein assembly
Protein Complex Page Updates
December 01, 2021
SGD has updated our protein complex pages to have the same format as gene pages, with tabs across the top for each category of information, including a Summary page, a new Gene Ontology page, and a new Literature page for each complex. Just as we do for all of your favorite genes, Gene Ontology and Literature curation for complexes will be ongoing.
If you have any questions or feedback about the updates to our complex pages, please do not hesitate to contact us at any time.
Categories: Announcements, Data updates, Website changes
Tags: protein complex, Saccharomyces cerevisiae
New links to AlphaFold 3D Predicted Protein Structure Database
November 09, 2021
Would you like to see the shape of your protein?
SGD now contains links to AlphaFold in the Resources section of the Summary, Protein and Homology pages for every gene.
- The links through SGD give quick access to EMBL–European Bioinformatics Institute‘s new, highly accurate tool for predicting protein structure.
- Given a peptide sequence for an uncharacterized protein, AlphaFold will model predicted domains and provide relative confidence levels for each portion of the prediction.
- The predicted domains can then be compared to known protein structures (using a tool such as PDBeFold to seek matches to characterized protein families).
- Whether or not a family is identified, the comparison will yield clues to protein function to help design the next experiments.
Categories: Data updates
Updates to legacy gene names
November 05, 2021
SGD has long been the keeper of the official Saccharomyces cerevisiae gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years.
The accepted format for gene names in S. cerevisiae comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the “Name Description” in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example “ADE” for “ADEnine biosynthesis” or “CDC” for “Cell Division Cycle”. Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an ORF, a tRNA, another type of non-coding RNA, an ARS, or a genetic locus. Some S. cerevisiae gene names that pre-date the current nomenclature standards do not conform to this format, such as MRLP38, RPL1A, and OM45.
A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.
| ORF | Old gene name | New gene name |
|---|---|---|
| YGL234W | ADE5,7 | ADE57 |
| YER069W | ARG5,6 | ARG56 |
| YBR208C | DUR1,2 | DUR12 |
| YIL154C | IMP2′ | IMP21 |
Categories: Announcements, Data updates
Tags: gene nomenclature
Reference Genome Annotation Update R64.3
August 03, 2021
The S. cerevisiae strain S288C reference genome annotation was updated in its first major update since 2014. The new genome annotation is release R64.3, which released on April 21, 2021. Note that the underlying sequence of 16 assembled nuclear chromosomes, plus the mitochondrial genome, remained unchanged in annotation release R64.3.1 (relative to genome sequence release R64.2.1).
This annotation update included:
- 7 new ORFs: OTO1/YGR227C-A, YHR052C-B, YHR054C-B, YJR107C-A, YKL104W-A, YLR379W-A, YMR008C-A
- 5 new ncRNAs: GAL10-ncRNA, TBRT/XUT_2F-154, SUT169, PHO84 lncRNA, GAL4 lncRNA
- 2 new uORFs for ROK1/YGL171W
- 1 new recombination enhancer: RE
- 1 new LTR: YELWdelta27
- 3 ORFs with shifted translation starts: HPA3/YEL066W, YJR012C, LTO1/YNL260C
- 1 ORF with shifted translation stop plus new intron: LDO45/YMR147W
- Changed feature_type (and SO_term) for non-transcribed spacers: NTS1-2, NTS2-1, NTS2-2
- New systematic nomenclature system for entire annotated complement of ncRNAs
Various sequence and annotation files are available on SGD’s Downloads site. You can find more update details and read about the new systematic nomenclature system for noncoding RNA genes on the Details of 2021 Reference Genome Annotation Update R64.3 SGD Wiki page.
Categories: Data updates
SGD Homology Data Now Available On New Homology Pages
March 25, 2021
SGD is excited to introduce our new Homology Pages! These pages can be accessed by clicking on the Homology tab in the header of SGD gene pages, as seen below.
The information displayed on the Homology Pages is divided into several sections:
- Homologs: Information about known homologs for the gene of interest, such as the species of the homolog, the corresponding Gene ID from the Alliance of Genome Resources, and the name of the homolog.
- Functional Complementation: Data about cross-species functional complementation between yeast and other species, curated by SGD and the Princeton Protein Orthology Database (P-POD).
- Fungal Homologs: Curated homolog information for 24 additional species of fungi. View the species of the fungal homolog, the database source of the entry, and the Gene ID of the homolog from that database.
- External Identifiers: A list of external identifiers for the protein from various database sources.
If you have any questions or feedback regarding our new Homology Pages, please do not hesitate to contact us at any time.
Categories: Data updates, Homologs, New Data, Yeast and Human Disease
Interactions Page Updates
November 06, 2020
SGD has made recent updates to our Gene Interactions Page for improved clarity. Previously, genetic and physical interaction annotations were combined in one table, but now these annotations are recorded in separate annotation tables. The menu in the top left corner can be used to view and navigate to each section of the Interactions page.
Additionally, alleles, SGA Scores, and P-values are now included for annotations from the global interactions paper by Costanzo M, et al. (2016).
Please be sure to watch our Interactions Page Updates tutorial video for a quick walk-through of the changes:
If you have any questions or feedback about the updates to our Interactions Pages, please do not hesitate to contact us at any time.
Categories: Announcements, Data updates
Browse Metabolic Pathways at SGD
August 02, 2019
Did you know that SGD has over 200 curated biochemical pathways for you to explore? SGD’s YeastPathways is a database of metabolic pathways and enzymes in Saccharomyces cerevisiae. YeastPathways enables you to visualize yeast metabolism from large metabolic networks to individual pathways, and from biochemical reactions down to individual metabolites. Search tools and click-to-browse features in YeastPathways enable quick navigation and intuitive exploration of yeast metabolism.
As the first major content update to YeastPathways since 2012, we have recently updated 62 pathways with expertly-curated summaries on pathway biochemistry, genetics, regulation, and more. Compounds that were previously missing a structure have also now been updated, along with the stoichiometry and scheme of many pathway reactions. In addition to content updates, YeastPathways has also received a major software upgrade that provides new tools, pages, and visual aids.
With new content and software, YeastPathways is better than ever. Users new to YeastPathways will find that it’s easy to get started—simply access YeastPathways through the Function menu at SGD, then run a search for a pathway, compound, enzyme, or reaction on the YeastPathways homepage. You can also access YeastPathways through gene pages at SGD. Just run a search for your favorite metabolic enzyme at SGD (example: TPI1) and find the Pathways section on the locus summary page. Any pathways in which the protein is involved will be listed and linked to YeastPathways.
Check out YeastPathways and be sure to contact us if you have any questions or feedback!
Categories: Data updates
SK1 Sequence Updated in SGD
November 20, 2018
The alternative reference strain SK1 is a rapid and synchronously sporulating diploid constructed by Kane and Roth in the early 1970’s to study carbohydrate metabolism under sporulation conditions. Whereas the reference strain S288C is notorious for being poor at sporulation, SK1 undergoes sporulation readily, and as such has been widely used to study the genetics of sporulation and meiosis.
The genome of SK1, which was temporarily removed from SGD, is now available once again with an updated sequence provided by Scott Keeney from the Sloan Kettering Institute. You can access the updated SK1 sequence for your favorite genes from the Sequence tab, in the Alternative Reference Strains section (example: ECM22 Sequence page). To access the entire SK1 genome sequence, visit the SK1 Strain page.
In addition, we have updated following Sequence and Analysis tools to utilize the latest SK1 sequence:
Variant Viewer will be updated in a future release. Be sure to check out these updated tools and resources and let us know if you have any questions or comments.
Categories: Data updates, 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