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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.

Summary page and new Literature page

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: Saccharomyces cerevisiae, protein complex

New links to AlphaFold 3D Predicted Protein Structure Database

November 09, 2021

  • 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.
Structure of Hog1p

Categories: Data updates

Tags: new tools, AlphaFold

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.

ORFOld gene nameNew gene name
YGL234WADE5,7ADE57
YER069WARG5,6ARG56
YBR208CDUR1,2DUR12
YIL154CIMP2′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:

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 Newsletter, Spring 2021

May 27, 2021

About this newsletter: 

This is the Spring 2021 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this newsletter as well as previous newsletters on our Community Wiki.

Contents

  1. R64.3 Annotation Update
  2. New Homology Pages
  3. Functional Complementation Data Available on References Pages
  4. YeastMine Updates and New Templates
  5. Textpresso Central Update
  6. Number of Curated Alleles Continues to Grow
  7. Alliance of Genome Resources – Disease Associations for model organisms
  8. Fungal Pathogen Genomics Workshop

R64.3 Annotation Update

SGD curators periodically update the chromosomal annotations of the S. cerevisiae Reference Genome, which is derived from strain S288C.

The R64.3 annotation release, dated 2021-04-21, included various updates and additions:

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. 

New Homology Pages

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.
Image: 650 pixels
Image: 650 pixels

Functional Complementation Data Available on References Pages

Functional Complementation annotations are now viewable on reference pages for which there is curatable functional complementation data. This information describes cross-species functional complementation between yeast and other species, and is curated by SGD and the Princeton Protein Orthology Database (P-POD).

functional comp3.png

YeastMine Updates and New Templates

SGD has updated the current Gene–>UTRs YeastMine template with newly calculated 5′ and 3′ UTR sequence/coordinates. Additionally, transcript iso-forms for specific genes from the Pelachano et al., 2013 study can be accessed in YeastMine using the new Gene–>Transcripts template. Both templates can be found under the “Templates” section of YeastMine under the “Expression” category.

Transcript and UTR YeastMine Templates

Textpresso Central Update

Textpresso has recently been updated with a new system, adopting an overhauled user interface and introducing several new features including:

  • Search results shown in the context of the full text
  • Custom corpus creation
  • Customizable annotation interface
  • Search terms are highlighted in full-text view

Textpresso Central can also be accessed by clicking on “Full-text Search” under the Literature pull-down menu on the home page of SGD. More information about the changes and types of papers stored in Textpresso can be found in their About Us help section or (from Müller et al., 2018).

Number of Curated Alleles Continues to Grow

SGD now has approximately 13,000 alleles that are either fully or partially curated. To navigate to an allele page, use the search bar to find a specific allele or enter a gene name and select an allele from the autocomplete list. Additionally, these pages can be accessed by clicking on the allele name in a gene’s Phenotype Annotation table. SGD Curators continue to add new alleles or update existing ones as new information becomes available.

You can generate a list of all alleles in our database or find alleles for a specific gene using the Genes –> Alleles template in YeastMine. 

allele page.png

Alliance of Genome Resources – Disease Associations for model organisms

Did you know that you can find human disease associations for yeast genes and their orthologs in other key model organisms at the Alliance of Genome Resources?

SGD is a founding member of the Alliance of Genome Resources, which was established to facilitate the use of diverse model organisms in understanding the genetic and genomic bases of human biology, health, and disease.  Gene pages for yeast and other model organisms at the Alliance include a section for Disease Associations, including those for orthologous genes. Human diseases are represented using the Disease Ontology (DO).

allianceDiseaseTAZ1.png

Fungal Pathogen Genomics Workshop

From May 10th – 14th, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander were instructors for the Virtual Fungal Pathogen Genomics Workshop hosted by Wellcome Connecting Science. Our curators helped attendees learn more about the unique tools hosted on our website and provided them the opportunity to learn about other curation tools from FungiDB, EnsemblFungi, CGD, MycoCosm, and JGI. 

We would like to thank the Fungal Pathogen Genomics team for facilitating a successful virtual workshop, and for providing excellent training in web-based data mining resources for all attendees.

workshop.png

Categories: Newsletter

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, New Data, Homologs, Yeast and Human Disease

BREWMOR Workshop: Preparing Undergraduate Students for Research Experiences

February 03, 2021

BREWMOR: Bridging Research and Education With Model ORganisms (formerly BREW) will be hosting a virtual workshop titled, “Preparing Undergraduate Students for Research Experiences,” on Friday February 19th, 2021 from 4 – 6:30 PM US Eastern time.

After a very successful virtual BREW (Bridging Research and Education Workshop) in July of 2020 as part of the TAGC meeting, a steering committee was formed to coordinate activities of the BREW community. The name of the community was changed to BREWMOR: Bridging Research and Education With Model ORganisms, to include model organisms beyond yeast. 

A micro-BREWMOR event that will be held virtually on Friday February 19th, 2021 from 4-6:30 PM US Eastern time. The main purpose of the event is to provide a forum for social interactions and building a community for support and resource sharing.  The theme of this micro-BREWMOR will be “Preparing Undergraduate Students for Research Experiences”. The workshop will include a session related to the event’s main theme and opportunities to connect and collaborate with other undergraduate research mentors and teachers in multiple small breakout rooms focused on various topics.

Please register by February 8th at https://forms.gle/fdBCFxYjWuY38tSG6 . Registration is free. 

We hope you can join us at the micro-BREWMOR!

https://brewmor.weebly.com/gatherings.html

Categories: Announcements

Apply Now for the 2021 Fungal Pathogen Genomics (Virtual) Course

January 21, 2021

Fungal Pathogen Genomics is an exciting several day long course that provides experimental biologists working on fungal organisms with hands-on experience in genomic-scale data analysis. Through a collaborative teaching effort between the web-based fungal data mining resources FungiDB, EnsemblFungi, PomBase, SGD, CGD, MycoCosm, and JGI, students will learn how to utilize the unique tools provided by each database, develop testable hypotheses, and analyze various ‘omics’ datasets across multiple databases.

Please note: Due to the ongoing Covid-19 pandemic, the 2021 Fungal Pathogen Genomics course will be delivered in a virtual format.

Daily activities will include individual and group training exercises, supplementary lectures on bioinformatics techniques and tools used by various databases, and presentations by distinguished guest speakers covering the following topics:

  • Comparative genomics, gene trees, whole-genome alignment
  • Identification of orthologs and orthology-based inference
  • Genome browsers and gene pages
  • RNA-Seq analysis and visualization in VEuPathDB Galaxy
  • Variant calling analysis and Ensembl Variant Effect Predictor (VEP) tool
  • Development of advanced biologically relevant queries using FungiDB ‘search strategies’ and mining integrated datasets (proteomics, transcriptomics, phenotypes, etc.)
  • Genetic interactions, virulence genes, secondary metabolites
  • Overview of ontology structure, evidence, available tools, slimming and enrichment
  • Introduction to annotation and curation of fungal genomes (e.g. Apollo in EnsemblFungi, FungiDB, and MycoCosm/JGI)

The application deadline for the Fungal Pathogen Genomics workshop to be held May 10-14, 2021 in virtual format is February 18, 2021.

Don’t miss out – apply now!

Categories: Announcements

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