Maria: Created page with "Category:Newsletter '''About this newsletter:'''
This is the Spring 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users ab..."

2015-02-27T03:16:52Z

Created page with "Category:Newsletter '''About this newsletter:''' This is the Spring 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users ab..."

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[[Category:Newsletter]]
'''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.
You can also subscribe to SGD's RSS feed to receive updates on SGD news:
http://www.yeastgenome.org/feed 

==Announcing the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==
[[File:yeast-meet.jpg|center|600px]]
'''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.
Yours sincerely,
Duccio Cavalieri & Andriy Sibirniy (ICYGMB Organisers), on behalf of the National and International Organizing Committees.

[http://yeast2015.eu/ Registration and abstract submission are now open.] Follow [http://twitter.com/yeastgenome @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 [http://www.yeastgenome.org/strain/S288C/overview 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 [http://www.yeastgenome.org/cgi-bin/search/luceneQS.fpl?query=R64.2 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 ([http://www.yeastgenome.org/locus/S000002505/overview#sequence GRX3]/YDR098C and [http://www.yeastgenome.org/locus/S000003001/overview#sequence HOP2]/YGL033W), and 1 new ORF ([http://www.yeastgenome.org/locus/S000178054/overview RDT1]/YCL054W-A) and 4 RNAs ([http://www.yeastgenome.org/locus/S000144908/overview RME2], [http://www.yeastgenome.org/locus/S000144910/overview RME3], [http://www.yeastgenome.org/locus/S000178119/overview IRT1], [http://www.yeastgenome.org/locus/S000077071/overview ZOD1]) were added to the genome annotation. Other additions include 8 nuclear [http://www.yeastgenome.org/cgi-bin/search/luceneQS.fpl?query=etc matrix attachment sites], and 8 mitochondrial [http://www.yeastgenome.org/cgi-bin/search/luceneQS.fpl?query=Mitochondrial+origin+of+replication 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 [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl Summary of Chromosome Sequence and Annotation Updates].

The R64.2.1 annotation release is submitted to GenBank and tracked with Assembly accession [http://www.ncbi.nlm.nih.gov/assembly/GCA_000146045.2/ GCA_000146045.2]. The identical assembly and annotation is copied into NCBI's RefSeq dataset, under Assembly accession [http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2/ 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 [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page. All SGD videos are also available through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.

Please stay tuned over the coming weeks as we add more videos, and please [http://www.yeastgenome.org/suggestion 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:
*[http://www.yeastgenome.org/reference/12872131/overview Peng et al. 2003]
*[http://www.yeastgenome.org/reference/14557538/overview Hitchcock et al. 2003]
*[http://www.yeastgenome.org/reference/18433149/overview Seyfried et al. 2008]
*[http://www.yeastgenome.org/reference/19837041/overview Vogtle et al. 2009]
*[http://www.yeastgenome.org/reference/21427232/overview Ziv et al. 2011]
*[http://www.yeastgenome.org/reference/22729381/overview Mommen et al. 2012]
*[http://www.yeastgenome.org/reference/22865919/overview Henriksen et al. 2012]
*[http://www.yeastgenome.org/reference/23749301/overview Swaney et al. 2013]
*[http://www.yeastgenome.org/reference/23793018/overview Kolawa et al. 2013]
*[http://www.yeastgenome.org/reference/23954790/overview Weinert et al. 2013]
*[http://www.yeastgenome.org/reference/25109467/overview 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 [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinMods&scope=all Gene -> Protein Modifications] template of
SGD’s advanced search tool, [http://yeastmine.yeastgenome.org/yeastmine/templates.do YeastMine]. 

We have also added experimentally-determined amino-terminal sequence and acetylation data from two publications: [http://www.yeastgenome.org/reference/19837041/overview Vogtle et al. 2009] and [http://www.yeastgenome.org/reference/22729381/overview Mommen et al. 2012]. These data can be accessed via YeastMine using the [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinMods_Ntermini Gene -> Experimental N-termini and N-terminal modifications] template.
Lastly, two new templates allow easy retrieval of protein abundance data curated from [http://www.yeastgenome.org/reference/14562106/overview Ghaemmaghami et al. 2003]. These data are also displayed on the Protein pages of individual proteins. The [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinAbundance&scope=all Gene -> Protein Abundance] template retrieves molecules/cell counts for a gene or list of genes. The same data can be quickly filtered using the [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Genes_Proteins_AbundanceRange&scope=all Retrieve -> Proteins in a given molecules/cell abundance range] template.
Please explore these new data and YeastMine templates, and [http://www.yeastgenome.org/cgi-bin/suggestion 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”:
*[http://www.yeastgenome.org/strain/CENPK/overview CEN.PK]
*[http://www.yeastgenome.org/strain/D273-10B/overview D273-10B]
*[http://www.yeastgenome.org/strain/FL100/overview FL100]
*[http://www.yeastgenome.org/strain/JK9-3d/overview JK9-3d]
*[http://www.yeastgenome.org/strain/RM11-1a/overview RM11-1a]
*[http://www.yeastgenome.org/strain/SEY6210/overview SEY6210]
*[http://www.yeastgenome.org/strain/SK1/overview SK1]
*[http://www.yeastgenome.org/strain/Sigma1278b/overview Sigma1278b]
*[http://www.yeastgenome.org/strain/W303/overview W303]
*[http://www.yeastgenome.org/strain/X2180-1A/overview X2180-1A]
*[http://www.yeastgenome.org/strain/Y55/overview Y55]
These genomes are accessible via [http://www.yeastgenome.org/locus/ste6/sequence Sequence], [http://www.yeastgenome.org/strain/SK1/overview Strain], and [http://www.yeastgenome.org/contig/JRIH01000182.1/overview 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; [http://www.yeastgenome.org/strain/S288C/overview 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 [http://www.yeastgenome.org/cgi-bin/blast-sgd.pl BLAST] datasets, multiple sequence [http://www.yeastgenome.org/cgi-bin/FUNGI/alignment.pl?locus=ste6 alignments], the [http://www.yeastgenome.org/cgi-bin/PATMATCH/nph-patmatch Pattern Matching] tool, and the [http://www.yeastgenome.org/download-data/sequence Downloads] site. Please explore these new genomes, and [http://www.yeastgenome.org/cgi-bin/suggestion send] us your feedback.

== Links to New Software and Resource in Community Wiki ==
*[http://www.massgeneral.org/cancer/research/motamediresources.aspx 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.

*[http://www.massgeneral.org/cancer/research/motamediresources.aspx 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 [http://wiki.yeastgenome.org/index.php/Methods Methods] page of the Community Wiki.

The publication describing the software and the primers it generated is [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116657 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. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''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 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']

==Upcoming Meetings==

*[http://www.Hendrix.edu/SERYM SERYM 2015: 22nd Annual Southeastern Regional Yeast Meeting]
:William J. Clinton Presidential Center, Little Rock, AR 
:March 17-22, 2015

*[http://www.genetics-gsa.org/fungal/2015/ 28th Fungal Genetics Conference]
:Pacific Grove, CA
:March 17-22, 2015

*[http://www.byg2015.ls.manchester.ac.uk The British Yeast Group (BYG) Meeting 2015]
:University of Manchester, Manchester, UK
:March 25-27, 2015

*[http://biocuration2015.big.ac.cn/ Biocuration 2015]*
:Beijing, China
:April 23-26, 2015

*[http://www.taosciences.it/ssbss2015/ Synthetic and Systems Biology Summer School: Biology meets Engineering and Computer Science - 2nd Edition]
:Taormina, Sicily, Italy
:July 5-9, 2015

*[http://meetings.cshl.edu/courses/2015/c-yeas15.shtml Yeast Genetics & Genomics Course]
:Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
:July 21 - August 10, 2015

*[http://yeast2015.eu/ ICYGMB Conference (YEAST 2015): 27th International Conference on Yeast Genetics and Molecular Biology]*
:Levico Terme, Italy
:September 6-12, 2015

*[http://www.issy32.com/ 32nd International Specialized Symposium on Yeasts (ISSY32)]
:Perugia, Italy
:September 13-16, 2015
 *asterisks indicate attendance by SGD

== Stay connected to SGD ==
SGD is on [http://www.linkedin.com/company/saccharomyces-genome-database LinkedIn], [http://www.facebook.com/pages/Saccharomyces-Genome-Database-SGD/139140876128200 Facebook], [http://twitter.com/yeastgenome Twitter], [https://plus.google.com/104199722908489380865/posts Google+], and [http://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube]. Follow us to get updates on the latest developments at SGD and in the yeast community.
 
''Note: If you no longer wish to receive this newsletter, please contact the SGD Help Desk at [mailto:sgd-helpdesk@lists.stanford.edu sgd-helpdesk@lists.stanford.edu].''

SGD Quarterly Newsletter, Spring 2015 - Revision history

Maria: Created page with "Category:Newsletter '''About this newsletter:''' This is the Spring 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users ab..."

Maria: Created page with "Category:Newsletter '''About this newsletter:'''
This is the Spring 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users ab..."