SGD Quarterly Newsletter, Winter 2006
SGD Newsletter, February 2006
About this newsletter:
This is the February 2006 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 have received it because you are listed as a contact for SGD in our database.
Contents
- 1 Search for your Favorite Allele and more in 30,000+ Yeast-Related Full Text Articles
- 2 Several Sequence and Annotation Changes made to the Systematic Sequence of S. cerevisiae
- 3 SGD Publication Describes the Genome Snapshot Resource in the 2006 NAR Database Issue
- 4 FTP File Format Changes
- 5 Find Related Proteins in C. albicans and S. pombe Genomes
- 6 Links to Yeast Gene Order Browser Added
- 7 71 New Gene Summary Paragrpahs
- 8 Upcoming Conferences and Courses
Search for your Favorite Allele and more in 30,000+ Yeast-Related Full Text Articles
An allele, such as cdc28-1N, can be entered into the search box of SGD's full-text literature search powered by Textpresso. The full text of 30,000+ yeast-related articles will be searched to produce a list of references which mention this allele in the text or in a legend. The full-text literature search can be accessed via the Full-text search on the home page, as a link on the SGD Search Options and from the Literature pull-down menu on the right side of all Locus Summary Pages, where the search form is prefilled with the ORF or gene name.
Several Sequence and Annotation Changes made to the Systematic Sequence of S. cerevisiae
SGD curators have updated the systematic sequence and its annotation. Sequence and/or annotation changes were made affecting 43 features, and 18 new features have been added. Altered or new features are listed in the What's New in SGD for 2005 and 2006. Details regarding these changes can be found in the Table of Sequence Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly. The following table lists the sequence changes made during the last quarter.
| Chromosome | Sequence/Annotation Changes | New Features Added |
|---|---|---|
| I | SWH1/YAR042W | None |
| II | APE3/YBR286W | YBR056C-B, YBR201C-A, SNR161/snR161 |
| III | YCL048W-A, AGP1/YCL025C, ADF1/YCL058W-A | None |
| IV | YDR461C-A, YDR374W-A, YDR119W-A, YDL007C-A, NHP2/YDL208W, LSM6/YDR378C, RRP8/YDR083W | None |
| V | CHZ1/YER030W, RSM18/YER050C | SNR80/snR80 |
| VI | None | None |
| VII | SPG1/YGR236C, AMA1/YGR225W, YGR226C, CTT1/YGR088W | YGL194C-A |
| VIII | SAE3/YHR079C-A, SOL3/YHR163W, YHL026C | None |
| IX | SEC28/YIL076W, GPP1/YIL053W, CBR1/YIL043C | YIL102C-A |
| X | AIM22/YJL046W, JJJ2/YJL162C, ASG7/YJL170C | None |
| XI | UTH1/YKR042W, YKL023C-A, YKL065W-A, GLG1/YKR058W, PTM1/YKL039W, UTP11/YKL099C, CMC1/YKL137W | None |
| XII | YLR146W-A, REC102/YLR329W, DUS3/YLR401C | None |
| XIII | None | snR85, RNA170 |
| XIV | TRF5/YNL299W, YPT11/YNL304W | None |
| XV | CDC21/YOR074C, TMA46/YOR091W, MDM32/YOR147W, MCT1/YOR221C, MIP1/YOR330C, TMA16/YOR252W, FRE7/YOL152W | snR81 |
| XVI | JIP5/YPR169W, OAZ1/YPL052W, YPL052W-A | YPR145C-A |
| Mito | AI3/Q0060, AI4/Q0065 | None |
SGD Publication Describes the Genome Snapshot Resource in the 2006 NAR Database Issue
The 2006 Nucleic Acids Research Database issue features a paper (HTML|PDF) by the SGD staff describing the new Genome Snapshot resource at SGD.
FTP File Format Changes
The format of several sequence files on SGD's FTP site has been updated. All updated files are located in:
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/sequence/genomic_sequence/
The following changes have been made
1. Header lines in files found in the orf_dna, orf_protein, rna, and other_features subdirectories have been expanded:
- old 8-digit SGDIDs replaced with current 10-digit SGDIDs (the same number but with additional padding zeros)
- a detailed description of the feature, enclosed in quotes, is now included at the end of the header line
2. The content and header line format of the intergenic/NotFeature.fasta file have been changed:
- the intergenic sequences and coordinates listed no longer overlap with the flanking genes
- the header line lists the flanking genes
- the header format has been changed to be more consistent with those found in other sequence files
Find Related Proteins in C. albicans and S. pombe Genomes
The Model Organism BLASTP Best Hits resource now includes Candida albicans (CGD) and Schizosaccharomyces pombe (S. pombe GeneDB) in the list of model organisms whose predicted protein sequences have been compared to S. cerevisiae predicted protein sequences. This resource can be accessed from the "Comparison Resources" pull-down menu of the Locus Summary page and also from the Homology & Comparisons page. BLASTP Best Hits results are also available for download from SGD's FTP site.
Links to Yeast Gene Order Browser Added
The "Comparison Resources" pull-down menu (located on the right hand side of Locus Summary Pages) now includes links to the Yeast Gene Order Browser, a tool used to visualize the syntenic context of protein coding genes from S. cerevisiae, S. castellii, C. glabrata, A. gossypii, K. lactis, K. waltii, and S. kluyveri. This tool was developed by Kevin Byrne and Ken Wolfe (Trinity College, Dublin, Ireland), as described in Byrne and Wolfe.
71 New Gene Summary Paragrpahs
Gene Summary Paragraphs summarize published biological information for a gene and its product, 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 gene summary paragraphs for the following 71 genes have been added to their respective Locus Summary Pages.
List of Gene Summary Paragraphs Added During the Last Quarter
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
- XIIIth Southeastern Regional Yeast Meeting
- University of Southern Mississippi, Hattiesburg, MS
- April 1 - April 2, 2006
- British Yeast Group Meeting
- Pitlochry, UK
- April 10 - April 12, 2006
- ESF-EMBO Symposium on Gene Transcription in Yeast
- Application & abstract submission deadline: March 23rd, 2006
- Sant Feliu de Guixols, Spain
- June 24 - June 29, 2006
- 2006 Yeast Genetics and Molecular Biology Meeting*
- Princeton University, Princeton, NJ
- July 25 - July 30, 2006
- 24th Small Meeting on Yeast Transport and Energetics
- Prague, Czech Republic
- August 31 - September 3, 2006
- 5th International Meeting on Yeast Apoptosis
- Kutna Hora, Czech Republic
- September 3 - September 7, 2006
- XXIIIrd International Conference on Yeast Genetics and Molecular Biology*
- Melbourne, Australia
- July 1 - July 6, 2007
asterisks indicate attendance by SGD.*
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