SGD Quarterly Newsletter, Spring 2015
About this newsletter:
This is the Spring 2015 issue of the quarterly 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.
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Announcing the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)
From the ICYGMB Organizers:
It is our great pleasure to announce the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.
The conference is being co-organized by the Italian and the Ukrainian Scientific Committees under the auspices of the International Committee on Finances and Policy, together with the help of some international scientific societies such FEMS and EMBO.
The goal of the conference is to bring together investigators from around the world to present and discuss research focused on yeasts as model for the understanding of molecular biology and genetic processes, and as a paramount biotechnological microorganism.
Join us in this lovely part of the Trentino Region, in Italy, from 6th to 12th of September 2015 for this unique international event! Good science, food and location are waiting to make this a most memorable yeast Conference.
Duccio Cavalieri & Andriy Sibirniy (ICYGMB Organisers), on behalf of the National and International Organizing Committees.
Registration and abstract submission are now open. Follow @yeastgenome and #yeast2015 on Twitter for updates on the conference.
S. cerevisiae Reference Genome Annotation Update R64.2.1 - November 2014
SGD curators periodically update the chromosomal annotations of the S. cerevisiae Reference Genome, which is derived from strain S288C. Last November, the genome annotation was updated for the first time since the release of the major S288C resequencing update in February 2011. Note that the underlying sequence of 16 assembled nuclear chromosomes, plus the mitochondrial genome, remained unchanged in annotation release R64.2.1 (relative to genome sequence release R64.1.1).
The R64.2.1 annotation release included various updates and additions. The annotations of 2 existing proteins changed (GRX3/YDR098C and HOP2/YGL033W), and 1 new ORF (RDT1/YCL054W-A) and 4 RNAs (RME2, RME3, IRT1, ZOD1) were added to the genome annotation. Other additions include 8 nuclear matrix attachment sites, and 8 mitochondrial origins of replication. The coordinates of many autonomously replicating sequences (ARS) were updated, and many new ARS consensus sequences were added. Complete details can be found in the Summary of Chromosome Sequence and Annotation Updates.
The R64.2.1 annotation release is submitted to GenBank and tracked with Assembly accession GCA_000146045.2. The identical assembly and annotation is copied into NCBI's RefSeq dataset, under Assembly accession GCF_000146045.2.
SGD’s 60-second Help Videos
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out new videos available for our Interactions, Expression, and Phenotypes pages, accessible via the SGD Video Tutorials page. All SGD videos are also available through SGD’s YouTube channel.
Please stay tuned over the coming weeks as we add more videos, and please contact us if you have an idea for a great SGD 60-second Help!
New Protein Modification and Processing Data
Have you ever wondered what happens to your favorite protein after translation? We've added data on protein modification and processing to SGD, and made it easier for you to access all protein modification, processing, and abundance data.
We've captured phosphorylation, ubiquitination, succinylation, acetylation, and methylation data from the following 11 publications:
- Peng et al. 2003
- Hitchcock et al. 2003
- Seyfried et al. 2008
- Vogtle et al. 2009
- Ziv et al. 2011
- Mommen et al. 2012
- Henriksen et al. 2012
- Swaney et al. 2013
- Kolawa et al. 2013
- Weinert et al. 2013
- Wang et al. 2014
These data are shown on the Protein page for individual yeast proteins (in the Post-translational Modifications table located in the Sequence section of the page). They can also be retrieved in bulk using the new Gene -> Protein Modifications template of SGD’s advanced search tool, YeastMine.
We have also added experimentally-determined amino-terminal sequence and acetylation data from two publications: Vogtle et al. 2009 and Mommen et al. 2012. These data can be accessed via YeastMine using the Gene -> Experimental N-termini and N-terminal modifications template.
Lastly, two new templates allow easy retrieval of protein abundance data curated from Ghaemmaghami et al. 2003. These data are also displayed on the Protein pages of individual proteins. The Gene -> Protein Abundance template retrieves molecules/cell counts for a gene or list of genes. The same data can be quickly filtered using the Retrieve -> Proteins in a given molecules/cell abundance range template.
Please explore these new data and YeastMine templates, and send us your feedback.
New Alternative Reference Genomes
At SGD, we are expanding our scope to provide annotation and comparative analyses of all major budding yeast strains, and are making progress in our move toward providing multiple reference genomes. To this end, the following new S. cerevisiae genomes have been incorporated into SGD as “Alternative References”:Sequence, Strain, and Contig pages, and are the genomes for which we have curated the most phenotype data, and for which we aim to curate specific functional information. It is important to emphasize that we are not abandoning a standard sequence; S288C is still in place as “The Reference Genome”. However, we do recognize that it is helpful for students and researchers to be able to ‘shift the reference’, selecting the genome that is most appropriate and informative for a specific area of study.
These new genome sequences have been also been added to SGD’s BLAST datasets, multiple sequence alignments, the Pattern Matching tool, and the Downloads site. Please explore these new genomes, and send us your feedback.
Links to New Software and Resource in Community Wiki
- Genome Retrieval Script (GRS) is a Python-based customizable, open source code for genome analysis. GRS comes with detailed directions about how it can be modified to retrieve custom sequences from any annotated genome. A link to GRS can be found in the Software section of the Community WIki.
- PRIMED is a PRIMEr Database that was created using GRS. PRIMED contains the sequences of primers that can be used for deleting and C-terminally tagging every protein-coding gene in five of the most commonly used S. cerevisiae strains (S288C, RM11–1A, SK1, W303, and Y55) as well as S. pombe. In addition to protein-coding genes, the authors also provide the complete deletion primer set for deleting all noncoding RNAs in each genome. PRIMED has been tested for accuracy and is available for download in Excel format. A link to PRIMED is available on the Methods page of the Community Wiki.
The publication describing the software and the primers it generated is available in PLOS ONE.
Recent SGD Publications
- Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. Full-Text PDF | PMID: 25313161
- Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 Full-Text PDF | PMID: 25052702
- William J. Clinton Presidential Center, Little Rock, AR
- March 17-22, 2015
- Pacific Grove, CA
- March 17-22, 2015
- University of Manchester, Manchester, UK
- March 25-27, 2015
- Beijing, China
- April 23-26, 2015
- Synthetic and Systems Biology Summer School: Biology meets Engineering and Computer Science - 2nd Edition
- Taormina, Sicily, Italy
- July 5-9, 2015
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- July 21 - August 10, 2015
- ICYGMB Conference (YEAST 2015): 27th International Conference on Yeast Genetics and Molecular Biology*
- Levico Terme, Italy
- September 6-12, 2015
- Perugia, Italy
- September 13-16, 2015
*asterisks indicate attendance by SGD
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