SGD Quarterly Newsletter, Fall 2003

About this newsletter:
This is the November 2003 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.

As always, please contact SGD with any comments or suggestions at: yeast-curator@genome.stanford.edu

Improved gene product descriptions in SGD

SGD curators are in the process of revising the information currently associated with the Description field, for all protein-coding and non-coding RNA genes. This project will ensure that the Description, intended to be a concise summary of the function and biological context of each gene product, contains the most up-to-date information and is written in a consistent style. New Descriptions will be added to SGD gradually over the coming weeks.

Large-scale localization data added to SGD

Based on the genome-wide protein localization analysis published by Huh, et al. (Huh W.K. et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91) and protein abundance data published by Ghaemmaghami, et al. (Ghaemmaghami, S. et al. (2003) Global analysis of protein expression in yeast. Nature 425(6959):737-41), Cellular Component GO terms have been added for 1326 ORFs that were previously annotated to "cellular_component unknown". In addition, links to the Yeast GFP database are available on the pull-down menu on the right-hand side of each locus page. The complete set of localization and abundance data is available from the SGD ftp site. Thanks to Adam Carroll and the laboratories of Erin O'Shea and Jonathan Weissman for providing the data.

Sequence Similarity Query released

SGD has released the Sequence Similarity Query, a resource that displays the results of a sequence analysis performed quarterly at SGD. In this analysis, every protein sequence in S. cerevisiae is used as the query sequence for PSI-BLAST analysis against NCBI's non-redundant (nr) protein dataset. Available from the Comparison Resources pull-down menu on SGD locus pages, this resource provides a graphical summary of the PSI-BLAST results as well as options to view the alignment between the S. cerevisiae sequence and the sequences identified in the nr dataset.

Yeast-specific GO-Slim

SGD has created a yeast-specific GO-Slim. It contains a set of high level GO terms that best represent the major biological processes, functions, and cellular components that are found in S. cerevisiae. This 'goslim_yeast.2003' file is available for download from the Gene Ontology Consortium's ftp site. In addition, all yeast gene products (ORFs and RNAs) have been mapped to these GO-Slim terms in the 'go_slim_mapping.tab' file available from SGD's ftp site.

Addition of telomeric annotations

SGD has added annotations for the following features located at the ends of yeast chromosomes: Telomeric Region, X Element Combinatorial Repeat, X Element Core Sequence, Y' Element, and Telomeric Repeat. The annotation of these elements included developing a standardized nomenclature; see the Telomeric Elements section of SGD Gene Nomenclature Conventions for more information. Telomeric elements can be identified using the Find Chromosomal Features Search. Dave Barton and Ed J. Louis of the University of Leicester generously provided these data, as well as many suggestions for nomenclature and presentation.

Re-annotated translation start sites

Based on conservation between closely related Saccharomyces species, start site methionine codons for 77 open reading frames have been re-annotated. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein has been changed accordingly.

Protein Structure Viewer resource page

To address questions that we occasionally receive about the availability of protein structure viewers on various platforms, we created a protein viewer resource page. This page provides information about structural data in SGD as well as programs that are available for viewing, analyzing, and manipulating protein structures.

Gene Naming Guidelines updated

S. cerevisiae Gene Naming Guidelines were updated to incorporate changes agreed upon by the yeast community at the Cold Spring Harbor Yeast Cell Biology meeting (August 12-17, 2003). There were two revisions to the guidelines. First, for a reserved gene name to become a standard gene name, it must be published in a peer-reviewed journal article. Second, when a gene name reservation expires, the reservation will be removed if there is no response from the researcher for six months after the reservation has expired.

The Art of Brewing

SGD has added a presentation entitled "The Art of Brewing and the Biology of Lager Yeast" to the Yeast Virtual Library page. This presentation, which covers the brewing process, types of brewing yeasts, and yeast attributes of brewing interest, was kindly made available by Tom Pugh and David Ryder of Miller Brewing Company.

Corrections to Display of MIT Fungal Sequences

Due to errors at SGD, many of the flanking sequences described in Kellis et al. (Kellis M., et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54) were reported incorrectly on our website. For all genomes, the ORF coding sequences and their translations were always accurate. These incorrect data were present from July 4, 2003 to August 29, 2003.

Please note that this notice applies only to data from MIT; all data from Washington University were accurate as originally posted. The S. cerevisiae systematic sequence was always accurate, and as stated above, all ORF coding DNA sequences and their translations from the MIT data were always accurate.

Erroneous data included:

• All "upstream sequences" for ORFs encoded on the Crick strand.
• All "downstream sequences" for ORFs encoded on the Crick strand.
• Some "downstream sequences" or "upstream sequences" for ORFs encoded on the Watson strand, when located very close (< 1000 bp) to the end of a contig.

These incorrect data were displayed on SGD's "Fungal Alignment" pages and included in some ftp files. We have corrected the errors, and all sequences displayed in the Fungal Alignment are currently accurate. The ftp files have also been updated. These errors were entirely the responsibility of SGD and do not reflect upon the quality of the MIT data. We deeply regret these mistakes and apologize for any inconvenience they may have caused.

Incorrect Codon Usage Values and Motif Predictions

The Protein Info pages for some ORFs (473 total) have displayed incorrect values for Codon Adaptation Index (CAI), Codon Bias Index (CBI), and Frequency of Optimal Codon usage (FOP) due to incorrect calculation of these values for newly added ORFs and for existing ORFs after changes to the protein sequence (due either to a change in the sequence or to a change in the start or stop site annotated for the ORF). Some of these ORFs may have also displayed inaccurate predictions of signal peptides and transmembrane domains because the predictions were not updated when the ORF boundaries or sequences were changed. These values were corrected on October 23rd, 2003.

Upcoming Conferences and Courses

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

• March 24-28, 2004: Physiology of Yeast and Filamentous Fungi at Anglet, France.

• July 10-15, 2004: Yeast Chromosome Structure, Replication and Segregation at Callaway Gardens, Pine Mountain, GA.

• July 25-August 1, 2004: Yeast Genetics & Molecular Biology at University of Washington, Seattle, WA.

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