Kyla at 22:33, 19 December 2013

2013-12-19T22:33:11Z

Kyla: Created page with "Category:Newsletter
'''About this newsletter:'''

This is the May 2007 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our use..."

2013-12-19T20:08:06Z

Created page with "Category:Newsletter '''About this newsletter:''' This is the May 2007 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our use..."

New page

[[Category:Newsletter]]
 '''About this newsletter:''' 
 This is the May 2007 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 

 Details of these items can be viewed at the [http://www.yeastgenome.org/blog SGD Blog] 

==Community Wiki Available==
In order to facilitate sharing of information about ''S. cerevisiae'' genes, gene products, and resources within the yeast community, SGD now includes a [http://wiki.yeastgenome.org/index.php/Main_Page Community Wiki]. Like the popular Wikipedia, the SGD Community Wiki is a set of web pages that allow users to easily add and edit information. This Community Wiki has been pre-loaded with basic locus information from SGD as well as user annotations previously submitted through the Community Annotation pages. We invite the research community to further develop and enhance the information on the wiki pages. For example, the Wiki would be the ideal place to share comments on particular deletion strains or record differences in mutant phenotypes in different strain backgrounds. Links are available in the "Additional Information" section and from the "Literature" pull-down of each Locus Summary page as well as on the Community Info contents page.
==Nucleotide-level Variation Among Commonly Used Yeast Strains==
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=17389913 Schacherer et al.] identify SNPs between S288c and seven commonly used lab strains; these data are available on the SGD FTP site and can be searched and viewed online via the [http://gbrowse.princeton.edu/cgi-bin/gbrowse/yeast_strains_snps/ Yeast SNPs Browser] available at Princeton University.
==New or Updated 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 (February - April 2007), new summary paragraphs for the following 695 features have been added to their respective Locus Summary pages.

:::::: '''List of Summary Paragraphs Added During the Last Quarter''' 
{| class="wikitable"
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YNL220W#summaryparagraph ADE12/YNL220W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR359W#summaryparagraph ADE13/YLR359W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YFL030W#summaryparagraph AGX1/YFL030W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDL132W#summaryparagraph CDC53/YDL132W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YER166W#summaryparagraph DNF1/YER166W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR093W#summaryparagraph DNF2/YDR093W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YMR162C#summaryparagraph DNF3/YMR162C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YAL026C#summaryparagraph DRS2/YAL026C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YCR075C#summaryparagraph ERS1/YCR075C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YFR019W#summaryparagraph FAB1/YFR019W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YBR140C#summaryparagraph IRA1/YBR140C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YOL081W#summaryparagraph IRA2/YOL081W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YGL035C#summaryparagraph MIG1/YGL035C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YGL106W#summaryparagraph MLC1/YGL106W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YPR188C#summaryparagraph MLC2/YPR188C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YMR167W#summaryparagraph MLH1/YMR167W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YIL048W#summaryparagraph NEO1/YIL048W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=NME1#summaryparagraph NME1] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YBR295W#summaryparagraph PCA1/YBR295W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR145W#summaryparagraph RMP1/YLR145W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLL002W#summaryparagraph RTT109/YLL002W] || SDO1/YR002W || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR478W#summaryparagraph SNM1/YDR478W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YJR104C#summaryparagraph SOD1/YJR104C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR362W#summaryparagraph STE11/YLR362W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YHL007C#summaryparagraph STE20/YHL007C] || 85 RPL genes || 56 RPS genes || 7 RPP genes || 50 Retrotransposons
|-
| 382 Long Terminal Repeats || 89 Transposable Element Genes || || ||
|}
==GO Annotations from GOA-UniProt Added==
SGD has incorporated manual GO annotations for ''S. cerevisiae'' proteins from the [http://www.ebi.ac.uk/GOA GO Annotation (GOA) project] at EBI. These annotations can be identified at SGD by the source, e.g., 'UniProt', displayed on the 'Assigned By' column of the GO evidence and references page. The GO evidence and references page can be accessed by clicking on the 'Gene Ontology' tab from any Locus Summary page (e.g., please see [http://www.yeastgenome.org/cgi-bin/GO/goAnnotation.pl?dbid=S000000648 Gene Ontology evidence and references page for RSC6]). The gene_associations.sgd file, which provides a complete set of manual GO annotations for ''S. cerevisiae'', now includes these annotations from the GOA UniProt file.
==5' UTR introns Added==
Locus Summary page annotation has now been expanded to include introns located in the 5'-untranslated regions (5' UTRs) of primary transcripts. The Advanced Search can be used to obtain a complete list of genes with 5' UTR introns. We thank the many researchers who generated these data and reviewed our incorporation of it, including Manny Ares, Paul Cliften, Zhihong Zhang, Kara Juneau, and Takashi Ito.
==Sequence and Annotation Updates==
As new data become available, SGD curators update the systematic sequence and its annotation. Information regarding sequence and annotation changes can be found via the [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl Summary of Chromosome Sequence and Annotation Updates] and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly. During the last quarter (February - April 2007), sequence and annotation changes were made affecting 37 features and 11 new features were added.
{| class="wikitable"
|-
! Chromosome !! Sequence/Annotation Changes !! New Features Added
|-
| I || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=HRA1 HRA1], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YAL004W YAL004W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YAL005C SSA1/YAL005C] || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS102 ARS102], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS103 ARS103], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS105 ARS105], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS108 ARS108], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS109 ARS109], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS111 ARS111], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS112 ARS112]
|-
| II || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YBLCtau1 YBLCtau1], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YBRCtau2 YBRCtau2], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YBLCdelta7 YBLCdelta7], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YBRCdelta11 YBRCdelta11], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YBRCdelta14 YBRCdelta14], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YBRCdelta19 YBRCdelta19] || None
|-
| III || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS317 ARS317], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YCLCdelta1 YCLCdelta1], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YCRCdelta14 YCRCdelta14], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YCRCdelta6 YCRCdelta6], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YCRCdelta7 YCRCdelta7] || None
|-
| IV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snR47 snR47], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YDRCsigma4 YDRCsigma4], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YDRWsigma2 YDRWsigma2], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS416 ARS416], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS404 ARS404] || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS400 ARS400]
|-
| V || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YERCdelta8 YERCdelta8] || None
|-
| VI || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YFR045W YFR045W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS601 ARS601], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS602 ARS602], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS604 ARS604], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS605 ARS605],[http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS606 ARS606], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS607 ARS607], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS608 ARS608], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS609 ARS609], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS603.5 ARS603.5], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS603 ARS603] || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ARS610 ARS610]
|-
| VII || None || None
|-
| VIII || None || None
|-
| IX || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YILWdelta2 YILWdelta2] || None
|-
| X || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YJRCdelta19 YJRCdelta19], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YJRCdelta16 YJRCdelta16], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YJRCdelta15 YJRCdelta15] || Example
|-
| XI || None || None
|-
| XII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YLRWdelta24 YLRWdelta24] || ARS1200
|-
| XIII || None || None
|-
| XIV || None || None
|-
| XV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YOR396W YRF1-8/YOR396W] || None
|-
| XVI || None || None
|}
==Upcoming Conferences and Meetings==
Information on registration and abstract deadlines for the following conferences is available at:
http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

*The Biology of Genomes*
:Cold Spring Harbor Laboratory, New York
:May 8 - 12, 2007

*Fourth International Fission Yeast Meeting*
:Copenhagen, Denmark
:June 11 - 16, 2007

*Conference on Physiology of Yeasts and Filamentous Fungi (PYFF3)
:Helsinki, Finland
:June 13 - 16, 2007

*XXIIIrd International Conference on Yeast Genetics and Molecular Biology*
:Melbourne, Australia
:July 1 - 6, 2007

*Yeast Cell Biology*
:Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
:August 15 - 19, 2007
:Abstract Deadline: May 23, 2007

*ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution
:Hotel Eden Roc, Sant Feliu de Guixols (Costa Brava), Spain
:October 20 - 25, 2007
:Abstract Deadline: August 1, 2007

*Genome Informatics*
:Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
:November 1 - 5, 2007
:Abstract Deadline: August 1, 2007

 asterisks indicate attendance by SGD.* 
 '''Manage your subscription''' 
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@@ Line 2: / Line 2: @@
 <br>'''About this newsletter:'''<br \>
 <br>This is the May 2007 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<br \>
 ==Community Wiki Available==
 In order to facilitate sharing of information about ''S. cerevisiae'' genes, gene products, and resources within the yeast community, SGD now includes a [http://wiki.yeastgenome.org/index.php/Main_Page Community Wiki]. Like the popular Wikipedia, the SGD Community Wiki is a set of web pages that allow users to easily add and edit information. This Community Wiki has been pre-loaded with basic locus information from SGD as well as user annotations previously submitted through the Community Annotation pages. We invite the research community to further develop and enhance the information on the wiki pages. For example, the Wiki would be the ideal place to share comments on particular deletion strains or record differences in mutant phenotypes in different strain backgrounds. Links are available in the "Additional Information" section and from the "Literature" pull-down of each Locus Summary page as well as on the Community Info contents page.

SGD Quarterly Newsletter, Spring 2007 - Revision history

Kyla at 22:33, 19 December 2013

Kyla: Created page with "Category:Newsletter '''About this newsletter:''' This is the May 2007 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our use..."

Kyla: Created page with "Category:Newsletter
'''About this newsletter:'''

This is the May 2007 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our use..."