SGD Quarterly Newsletter, Winter 2011

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About this newsletter:

This is the Winter 2011 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:

Reference Sequence Updated

The budding yeast Saccharomyces cerevisiae reference genome sequence was updated on February 3, 2011. This is the first major update of the S288C reference sequence since 1996, and 194 proteins have changed as a result of this update. The new version, called "S288C 2010", was provided by Fred Dietrich of Duke University, and was determined using new high fidelity sequencing from an individual yeast colony. This update increases accuracy by using modern sequencing technology (Illumina HiSeq) and provides a valuable resource that will serve as the reference point from which to expand our annotation of additional S. cerevisiae strains. In the very near future, SGD will provide researchers with the genome sequences for several commonly used laboratory strains. This is a very exciting time. We will soon have the sequence of all major laboratory strains and hundreds of wild and commercial isolates. Comparative genomics with so many well-studied S. cerevisiae strains and closely-related species will enhance the awesome power of yeast genomics.

YeastMine Updated

YeastMine, a powerful data search and retrieval tool, has been upgraded to InterMine version 0.95. This software update includes many new features, improvements and bug fixes. Key new features include a completely redesigned homepage, a more powerful multifaceted keyword search and template ranking by frequency of search. In addition, new pre-defined search templates have been added and YeastMine can now be used to query the following datatypes: chromosomal features, protein features, GO annotations, phenotypes, interaction data and curated literature. YeastMine will soon replace several search tools at SGD. Please explore its powerful query options and send us feedback.

YeastMine was created through an NIH funded collaboration between InterMine, the Rat Genome Database (RGD), and the Zebrafish Model Organism Database (ZFIN) to provide interoperability between model organism databases.

SGD's Batch Download Tool to be Retired

SGD's Batch Download tool will be retired soon, because all of its functions and many more can now be accomplished via YeastMine, which offers flexible queries and fast retrieval of multiple datatypes from SGD for a custom list of genes or proteins. Please contact us if you have any concerns.

New Gene Summary Paragraphs

Summary Paragraphs summarize published biological information for a gene/feature, and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the last quarter new summary paragraphs have been added to their respective Locus Summary pages for 10 features. Genes with new summary paragraphs are reported weekly on SGD's "What's New" page.

Upcoming Conferences and Meetings

Information on registration and abstract deadlines for the following conferences is available on the SGD Wiki.

  • 18th Anual Southeastern Regional Yeast Meeting (SERYM)
Mississippi State University, Mississippi
March 11-13, 2011
  • 26th Fungal Genetics Meeting (GSA)
Asilomar Conference Center, Pacific Grove, CA
March 15-20, 2011
  • British Yeast Group Meeting (BYG 2011)
Brighton, United Kingdom
March 23-25, 2011
  • 52nd Annual Drosophila Research Conference (GSA)
Town & Country Resort & Conference Center, San Diego, CA
March 30 - April 3, 2011
  • 8th International Meeting on Yeast Apoptosis (IMYA)
Canterbury, Kent, United Kingdom
May 2-6, 2011
  • Telomeres & Telomerase
Cold Spring Harbor Labs, CSH, NY
May 3-7, 2011
  • Omics Meets Cell Biology
Keystone Symposia, Alpbach, Austria
May 8-13, 2011
  • The Biology of Genomes
Cold Spring Harbor Labs, CSH, NY
May 10-14, 2011
  • 10th Yeast Lipid Conference
University of Oulu, Oulu, Finland
May 26-28, 2011
  • International C. elegans Meeting (GSA)
UCLA, Los Angeles, CA
June 22-26, 2011
  • 25th International Conference on Yeast Genetics and Molecular Biology
Olsztyn, Poland
July 11-16, 2011
  • Yeast Cell Biology
Cold Spring Harbor Labs, CSH, NY
August 16-20, 2011
  • Comparative genomics of eukaryotic microorganisms: understanding the complexity of diversity
Sant Feliux, Spain
October 15-20, 2011

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