SGD Quarterly Newsletter, Spring 2010

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About this newsletter:

This is the April 2010 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:

New article about curation published in Molecular Genetics and Genomics

The process of literature curation is described in Hirschman, et al., A MOD(ern) perspective on literature curation, Mol Genet Genomics (2010), written by four curators from SGD, TAIR (The Arabidopsis Information Resource), ZFIN (The Zebrafish Information Network), and MGI (Mouse Genome Informatics). This perspective discusses how papers are identified and prioritized for curation, some of the challenges MOD curators face, and ways in which researchers and publishers can support the work of curators. Hirschman et al. 2010:

Additional DNA binding site motifs added

DNA binding site motif sequences, as described in Zhu, et al. (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors, Genome Res. 19:556, have been added to the "Regulatory Role" section of the Locus Summary pages of 89 known and predicted transcription factors (for an example, see NDT80). Each binding site sequence is accompanied by a link to search intergenic regions in the genome for all such motifs. Thanks to Kimberly Robasky and Martha Bulyk for providing the data. NDT80 Locus Summary page:

Curation Focus: RNA polymerases I, II, and III

Yeast cells have three nuclear RNA polymerases that are conserved in all eukaryotes. RNA polymerase I produces the major ribosomal RNA transcript. RNA polymerase II produces all mRNAs and most of the snRNAs and snoRNAs. RNA polymerase III produces the 5S rRNA, all tRNAs, and various other small RNAs. Information in SGD about the 31 genes (RET1, RPA12, RPA135, RPA14, RPA190, RPA34, RPA43, RPA49, RPB10, RPB11, RPB2, RPB3, RPB4, RPB5, RPB7, RPB8, RPB9, RPC10, RPC11, RPC17, RPC19, RPC25, RPC31, RPC34, RPC37, RPC40, RPC53, RPC82, RPO21, RPO26, and RPO31) encoding the subunits of these three RNA polymerase complexes has recently been reviewed and updated, including their descriptions, GO annotations, and mutant phenotypes, and Gene Summary Paragraphs have been added to their Locus Summary pages.

MochiView motif analysis and genome browser software

A new platform-independent Java genome browser and motif analysis software called MochiView has recently been released. Originally designed for visualization and analysis of ChIP-Chip data, MochiView allows motif analysis alone or in conjunction with ChIP-Seq/RNA-Seq data, and also with multiple additional genomes, including other fungi, humans, etc. It takes ~10 minutes to download the software and install the necessary genome sequence and gene information (using the GFF files stored on SGD, CGD, or AspGD). A manuscript describing the software has just been published in BMC Biology. For more information, please see the SGD wiki:

SGD's PSI-BLAST resource retired

SGD recently retired its PSI-BLAST (Position-Specific Iterated BLAST) resource. Similar queries can be performed at NCBI at the URL listed below. Click on "protein blast" in the "Basic BLAST" section, then select the PSI-BLAST algorithm. At SGD, an archived file from August 2009 containing the PSI-BLAST results of all S. cerevisiae ORFs as queries against the UniRef90 protein dataset from UniProt is available for download. BLAST at NCBI: Download archived PSI-BLAST results from SGD:

Come see us at YGM 2010

SGD representatives will be attending the 2010 Yeast Genetics & Molecular Biology Meeting in Vancouver at the end of July. We will present two posters and participate in a workshop ("SGD, other databases and computational tools") on Saturday afternoon. Please come by, say hello, complete our survey, and let us know how you use SGD. We would love to see you!

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 57 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 at:

  • The Biology of Genomes
Cold Spring Harbor, New York
May 11-15, 2010
  • Genetics 2010: Model Organisms to Human Biology
Boston, Massachusetts
June 12-15, 2010
  • EMBO Yeast Transcription Conference 2010
San Feliu de Guixols, Spain
June 19-24, 2010
  • Genetics of Industrial Microogransims
Melbourne, Austraila
June 28 - July 1, 2010
  • ISMB2010
18th Annual International Conference on Intelligent Systems for Molecular Biology
Boston, Massachusetts
July 11-13, 2010
  • MGED
13th Internation Meeting of the Microarray and Gene Expression Data Society
Boston, Massachusetts
July 13-15, 2010
  • Yeast Genetics and Molecular Biology Meeting
Vancouver, Canada
July 27 - August 1, 2010
  • Society for Industrial Microbiology 60th Annual Meeting
San Francisco, California
August 1-5, 2010
  • Systems Biology: Networks
Hinxton, UK
August 11-15, 2010
  • Genome Informatics
Hinxton, UK
September 15-19, 2010
  • XV International Conference on Yeast Genetics and Molecular Biology
Olsztyn, Poland
July 11-16, 2011

asterisks indicate attendance by SGD.*

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