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SGD Newsletter, December 2024

December 13, 2024

About this newsletter:
This is the December 2024 issue of the SGD newsletter. The goal of this newsletter is to inform SGD users about new features from SGD and to foster communication within the yeast community.

Contents

AlphaFold protein structures now on SGD protein pages

AlphaFoldSET1.png

We are thrilled to announce that we have now integrated AlphaFold protein structures into our protein pages! This cutting-edge addition provides detailed, high-accuracy 3D models of protein structures, offering invaluable insights into protein function and interactions. Researchers can now explore these comprehensive structural predictions directly within SGD, facilitating advanced studies in molecular biology and bioinformatics. Dive into the new AlphaFold protein structures and elevate your research with this powerful tool!

AlphaFold, developed by DeepMind, is an AI program that accurately predicts protein structures from amino acid sequences, enabling visualization of protein conformations.

The predicted structures can be accessed through the Protein Data Bank (PDB) and AlphaFold Protein Structure Database. Thanks to Kim Rutherford and Val Wood of Pombase for tips about adding AlphaFold structures to SGD.

YeastMine data available in AllianceMine

yeastmineLogo.png

Here at SGD we provide high-quality curated genomic, genetic, and molecular information on the genes and gene products of the budding yeast Saccharomyces cerevisiae. In 2011, SGD implemented InterMine, an open-source data warehouse system with a sophisticated querying interface, to better meet the complex and diverse needs of researchers searching and comparing data, resulting in the creation of YeastMine.

YeastMine is a multifaceted search and retrieval environment that provides access to diverse data types. Searches can be initiated with a list of genes, a list of Gene Ontology terms, or lists of many other data types. The results from queries can be combined for further analysis and saved or downloaded in customizable file formats. Queries themselves can be customized by modifying predefined templates or by creating a new template to access a combination of specific data types.

In July 2024, YeastMine was discontinued due to ongoing cuts in funding at SGD. However, we have moved the YeastMine data into AllianceMine, hosted by the Alliance of Genome Resources, of which SGD is a founding member. You can even access lists like “ALL_Verified_Uncharacterized_Dubious_ORFs” through the AllianceMine Lists just as you could in the previous versions of YeastMine. Ensure any bookmarks to YeastMine have been updated to match the new URL: https://www.alliancegenome.org/bluegenes/alliancemine. User documentation for the new YeastMine interface is available from InterMine.

Help maintain your genomic databases! Sign open letter supporting funding for biodata resources

FkAzFtQWIAExhDl.jpeg

The Global Biodata Coalition has an open letter campaign to show support for sustainable funding for biodata resources.

Please take a minute to read and sign- the form takes only seconds to fill out. Everyone – including students and postdocs, bioinformaticians and curators, PIs and directors – is invited to join those of us that have already added our signatures in support of the GBC. Find more information and sign at the GBC site.

Community wiki shutting down

As another casualty of decreased funding, SGD will no longer provide the Community Wiki. Some of the resources hosted on the wiki have been moved to our Help pages, the Alliance Community Forum, or remain available though the SGD downloads site. We thank all our past and current Community Wiki contributors, and invite the yeast community to join SGD on the Alliance Community forum.

SGD’s new GENETICS publication

geneticslogo.png

Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements has now been published in GENETICS and is available as an accepted manuscript. Check out the most recent updates at SGD, including the two most recent reference genome annotation updates, expanded biochemical pathways representation, changes to SGD search and data files, and other enhancements to the SGD website and user interface.

microPublications – Latest yeast papers

MicroPub.png

​microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.

Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.

Latest yeast microPublications:

All yeast microPublications can be found in SGD.

Alliance of Genome Resources – Latest Release 7.4

alliance logo.png

The Alliance of Genome Resources, a collaborative effort between SGD and other model organism databases (MODs), released version 7.4 in October 2024.

The 7.4.0 release includes ~2.5 million variants of clinical significance from ClinVar. The Alliance removed 400 million human variants from the search because their inclusion was hampering site performance. The removed variants are mostly of unknown or uncertain clinical significance. The Alliance has instead included over 2.5 million human variants of known clinical significance from ClinVar. This should speed up the performance of the search function and improve site stability. The Alliance will address inclusion of the other high throughput human variants in the future. More detailed information about the 7.4 Alliance release can be found in the release notes.

Give a Gift / Support SGD

gift.png

Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. Donations are now critical for our work to continue.

Your generous gift to SGD will help us to continue providing essential information for your research and teaching efforts.

To contribute, please make checks payable to Stanford University, noting that “the funds should be used to support the Saccharomyces Genome Database project, under the direction of Drs. Sherlock and Cherry in the Department of Genetics, Stanford University.  Account : GHJKO, Genetics : WAZC.”

Thank you for your support!

Kindly send by mail to:

Development Services
PO Box 20466
Stanford, CA 94309

CONTACT US: sgd-helpdesk@lists.stanford.edu

Upcoming conferences and courses

Happy Holidays from SGD!

SnowShmoo.png

We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 20th, and reopening on Monday, January 6th, 2025. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.

Note: If you wish to receive this newsletter by email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

Categories: Newsletter

AlphaFold protein structures now on SGD protein pages

November 18, 2024

We are thrilled to announce that we have now integrated AlphaFold protein structures into our protein pages! This cutting-edge addition provides detailed, high-accuracy 3D models of protein structures, offering invaluable insights into protein function and interactions. Researchers can now explore these comprehensive structural predictions directly within SGD, facilitating advanced studies in molecular biology and bioinformatics. Dive into the new AlphaFold protein structures and elevate your research with this powerful tool!

AlphaFold, developed by DeepMind, is an AI program that accurately predicts protein structures from amino acid sequences, enabling visualization of protein conformations. The predicted structures can be accessed through the Protein Data Bank (PDB) and AlphaFold Protein Structure Database.

Thanks to Kim Rutherford and Val Wood of Pombase for tips about adding AlphaFold structures to SGD.

Categories: Announcements

YeastMine shutting down July 15

July 01, 2024

Due to ongoing cuts to our funding, SGD can no longer continue to provide the YeastMine data warehouse resource. It is with heavy hearts that we discontinue this service.

Back in 2011, SGD implemented InterMine (http://www.InterMine.org), an open source data warehouse system with a sophisticated querying interface, to create YeastMine, a multifaceted search and retrieval environment that provided access to diverse data types. YeastMine served as a powerful search interface, a discovery tool, a curation aid, and a complex database presentation format.

YeastMine has served us all quite well. We are working to move the YeastMine data into AllianceMine, hosted by the Alliance of Genome Resources, of which SGD is a founding member.

To get started with AllianceMine, go to the Templates page, and filter by category = ‘YeastMine’.

Screenshot 2024-07-01 at 9.38.37 AM

Categories: Announcements

SGD Newsletter, Summer 2024

June 20, 2024

About this newsletter:
This is the Summer 2024 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 the SGD Community Wiki.

Contents

Give a Gift / Support SGD

gift.png

Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. Donations are now critical for our work to continue.

Your generous gift to SGD will help us to continue providing essential information for your research and teaching efforts. 

To contribute, please make checks payable to Stanford University, noting that “the funds should be used to support the Saccharomyces Genome Database project, under the direction of Drs. Sherlock and Cherry in the Department of Genetics, Stanford University.  Account : GHJKO, Genetics : WAZC.” 

Thank you for your support!

Kindly send by mail to:

Development Services
PO Box 20466
Stanford, CA 94309

CONTACT US: sgd-helpdesk@lists.stanford.edu

Reference genome update R64.5

SuperYeast.jpg

The S. cerevisiae strain S288C reference genome annotation has been updated to include previously unannotated features. The new genome annotation is release R64.5.1, dated 2024-05-29. Note that the underlying genome sequence itself was not altered; the chromosome sequences remain stable and unchanged.

The R64.5.1 update included:

Various sequence and annotation files are available on SGD’s Downloads site. You can find more update details on the Details of 2024 Reference Genome Annotation Update R64.5 SGD Wiki page.

Extended gene coordinates in GFF

The saccharomyces_cerevisiae.gff contains sequence features of Saccharomyces cerevisiae and related information such as Locus descriptions and GO annotations. The saccharomyces_cerevisiae.gff is fully compatible with Generic Feature Format Version 3, and is updated weekly.

In recent years, SGD has made two significant changes to the GFF content (described in more detail below):

  • In November 2020, SGD updated the file to reflect experimentally determined transcripts
  • In February 2024, SGD edited the ‘gene’ entries in the file to extend the coordinates to encompass the start and stop coordinates of the longest experimentally determined transcripts

In November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used. 

Starting November 2020: BDH2/YAL061W with rows for longest transcripts expressed in GAL and in YPD.

Then in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023). 

After February 2024: BDH2/YAL061W with expanded start/stop coordinates for ‘gene’, still with rows for longest transcripts expressed in GAL, YPD.

GFF is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.

Updates to SGD search

sgd maintenanceguy.jpeg

SGD is jam-packed with information, with new data being added every day. It’s a lot to keep up with, and with so much info, some inevitably ends up hidden from view. To make the various data types in SGD more readily accessible, we have made various improvements to the SGD search: 

  • New category for datasets. Over 3700 yeast datasets are accessible. Search by reference, keyword, assay, and lab.
  • New Strains subcategory for Reference search. Scroll down to ‘Associated Strains’ in the lefthand menu on the Search Results page.
  • Macromolecular complexes can now be searched with aliases. Further refine by reference, subunit, function, process, and location.
  • Search for alleles via their descriptions and SGDIDs. Drill down based on reference, allele type, gene, and phenotype.
  • RNA products can now be searched using RNAcentral IDs.

microPublications – latest yeast papers

MicroPub.png

​microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral. 

Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.

Latest yeast microPublications:

All yeast microPublications can be found in SGD.

Alliance of Genome Resources – Latest Release 7.2

alliance logo.png

The Alliance of Genome Resources, a collaborative effort between SGD and other model organism databases (MODs), released version 7.2 in June 2024.

The 7.2.0 release updates the Associated Alleles and Associated Models tables on Disease pages:

  • Each table has a new column, Disease Qualifier, with a working filter. The qualifier describes whether an allele or model may be, for example, implicated in the onset of a disease or a model for the severity of a disease, respectively
  • In addition to the Disease Qualifier, the Associated Models table now has new columns for Condition Modifier and Genetic Modifier
  • The “Annotation Details” pop-up has expanded to include more information.
    • Alleles table: Association, Genetic Modifiers, Genetic Sex, Notes, and Annotation Type
    • Models table: Genetic Sex, Notes, and Annotation Type
  • The Associated Models table now has working filters for the Experimental Condition, Condition Modifier, and Genetic Modifier columns, including the ability to filter on relationship (e.g. induced by) as well as content (e.g. “copper”)
  • The Download files from the disease page Associated Alleles table and Associated Models table now include additional information as well.
    • New columns and information for the Associated Alleles table include: Allele Association, Genetic Entity Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Genetic Sex, Notes, Annotation Type, Source URL, and Date.
    • New columns and information for the Associated Models table include: Model Type, Model Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Condition Modifiers, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Genetic Sex, Notes, Annotation Type, Source URL, and Date.

Upcoming conferences and courses

Categories: Newsletter

Reference Genome Annotation Update R64.5

June 19, 2024

The S. cerevisiae strain S288C reference genome annotation was updated. The new genome annotation is release R64.5.1, dated 2024-05-29. Note that the underlying genome sequence itself was not altered. The chromosome sequences remain stable and unchanged.

R64.5 Annotation update summary

This annotation update included (details in table below):

R64.5 Annotation update details

ChrFeatureDescription of changeReference
IIATG12/YBR217WNew uORF chrII:657824..657835, partially overlaps CDSYang Y, et al. (2023) PMID:35363116
IVYDL204W-ANew ORF chrIV:94133..94285Wacholder A, et al. (2023) PMID:37164009
VIYFR035W-ANew ORF chrVI:226260..226550Wacholder A and Carvunis AR (2023) PMID:38048358
VIIYGR016C-ANew ORF chrVII:523353..523246Wacholder A, et al. (2023) PMID:37164009, Chang S, et al. (2023) PMID:37927910
IXEFM4/YIL064WMove start 84 nucleotides downstream, new coordinates chrIX:242027..242716Hamey JJ, et al. (2024)PMID:38199565
IXYIL059CChange ORF qualifier from Dubious to Verified because stable translation product detectedWacholder A and Carvunis AR (2023) PMID:38048358
XIIIYMR106W-ANew ORF chrXIII:480924..481187Wacholder A and Carvunis AR (2023) PMID:38048358
XIVYNL040C-ANew ORF chrXIV:552558..552478Wacholder A, et al. (2023) PMID:37164009
XIVYNL155C-ANew ORF chrXIV:342135..341911Wacholder A and Carvunis AR (2023) PMID:38048358
XVATG19/YOL082WNew uORF chrXV:168632..168679Yang Y, et al. (2023) PMID:35363116
XVIATG5/YPL149W4 new uORFs: chrXVI:271236..271277, chrXVI:271252..271302, chrXVI:271299..271307, chrXVI:271302..271307Yang Y, et al. (2023) PMID:35363116
XVIATG13/YPR185WNew uORF chrXVI:907211..907351, partially overlaps CDSYang Y, et al. (2023) PMID:35363116

Categories: Data updates

Deadline extended to April 22 for the 2024 Yeast Genetics and Genomics Course

April 09, 2024

yeast_course_panorama

The application deadline for the 2024 Yeast Genetics and Genomics Course has been extended to April 22 – don’t miss your chance! Significant financial aid may be available for trainees applying, covering up to 50% of the cost of the course!

Find all the details and application form at the CSHL Meetings & Courses site.

For over 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory, though the name didn’t include “Genomics” in the beginning. The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists.

This year’s instructors – Grant Brown, Soni Lacefield, and Greg Lang – have designed a course (July 23 – August 13) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:

  • Transformation & Genome Engineering
  • Microscopy
  • Manipulating Yeast
  • Dissecting Tetrads
  • Isolating Mutants
  • Working with Essential Genes
  • Synthetic Genetic Arrays
  • Fluctuation Assays
  • Whole Genome Sequencing & Analysis
  • QTLMapping

Techniques have been summarized in the accompanying course manual, published by CSHL Press.

IMG_2185
There’s fierce competition between students at CSHL courses in the Plate Race, a relay in which teams carry stacks of 40 Petri dishes (used, of course).

Who should attend? Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics.

What else goes on there? Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also typically a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!

The Yeast Genetics & Genomics Course is loads of fun – don’t miss out!

Categories: Conferences

Tags: dna, genetics, genomics, science

New user interface for YeastMine

April 04, 2024

Here at SGD we provide high-quality curated genomic, genetic, and molecular information on the genes and gene products of the budding yeast Saccharomyces cerevisiae. Twelve years ago, in order to accommodate the increasingly complex and diverse needs of researchers for searching and comparing data, SGD implemented InterMine, an open source data warehouse system with a sophisticated querying interface, to create YeastMine.

Today’s news is that we have updated YeastMine to use the new BlueGenes user interface from InterMine. The new interface provides the same functionality you’re already familiar with, wrapped in a new design offering a more interactive experience for exploring and analyzing your data. We are making this switch because AllianceMine at the Alliance of Genome Resources, of which SGD is a founding member, is using the updated interface as well.

YeastMine is a multifaceted search and retrieval environment that provides access to diverse data types. Searches can be initiated with a list of genes, a list of Gene Ontology terms, or lists of many other data types. The results from queries can be combined for further analysis and saved or downloaded in customizable file formats. Queries themselves can be customized by modifying predefined templates or by creating a new template to access a combination of specific data types.

User documentation for the new YeastMine interface is available from InterMine.

Categories: Announcements

Tags: user-interface

Changes to Saccharomyces cerevisiae GFF3 file

March 01, 2024

The saccharomyces_cerevisiae.gff contains sequence features of Saccharomyces cerevisiae and related information such as Locus descriptions and GO annotations. It is fully compatible with Generic Feature Format Version 3. It is updated weekly.

After November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used. 

Old version: BDH2/YAL061W with longest transcripts expressed in GAL and in YPD.

Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition.  This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023). 

After February 2024: BDH2/YAL061W with increased start/stop coordinates.

This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.

Categories: Announcements, Data updates

Tags: biology, blog, genetics, news, Saccharomyces cerevisiae

Apply Now for the 2024 Yeast Genetics and Genomics Course

February 13, 2024

yeast_course_panorama

For over 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory, though the name didn’t include “Genomics” in the beginning. The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists.

The application deadline is March 31st, so don’t miss your chance!

Find all the details and application form at the CSHL Meetings & Courses site. This year’s instructors – Grant Brown, Soni Lacefield, and Greg Lang – have designed a course (July 23 – August 13) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:

  • Transformation & Genome Engineering
  • Microscopy
  • Manipulating Yeast
  • Dissecting Tetrads
  • Isolating Mutants
  • Working with Essential Genes
  • Synthetic Genetic Arrays
  • Fluctuation Assays
  • Whole Genome Sequencing & Analysis
  • QTLMapping

Techniques have been summarized in the accompanying course manual, published by CSHL Press.

IMG_2185
There’s fierce competition between students at CSHL courses in the Plate Race, a relay in which teams carry stacks of 40 Petri dishes (used, of course).

Who should attend? Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics.

What else goes on there? Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also typically a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!

The Yeast Genetics & Genomics Course is loads of fun – don’t miss out!

Categories: Conferences

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