View source for SGD Quarterly Newsletter, Spring 2008

[[Category:Newsletter]]
<br>'''About this newsletter:'''<br \>
<br>This is the April 2008 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 \>

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

==SGD RSS feed==
Updates and announcements from SGD are now available via our [http://www.yeastgenome.org/xml/SGD_RSS.shtml RSS feed] You can subscribe to our RSS feed using one of many RSS browsers. Some example browsers that are appropriate include FeedDemon, Firefox, Safari, Mac Mail version 3.1, and Google Reader.
==Post job opportunities==
Periodically SGD is asked to advertise job opportunities. In response, we have created a page in the [http://wiki.yeastgenome.org/index.php/Main_Page Community Wiki] to allow researchers to post [http://wiki.yeastgenome.org/index.php/Positions_in_yeast_labs positions available in their labs]. This page is linked from the [http://wiki.yeastgenome.org/index.php/Career_Resources Career Resources] page listed in the navigation menu. These pages can be edited by clicking the "edit" tab at the top of the page.
==Community Wiki accessible from Wiki tab==
In order to increase accessibility to SGD's Community Wiki, a new Wiki tab has been added to the set of navigation tabs found at the top of the following pages: Locus Summary, Locus History, Literature Guide, Gene Ontology evidence and references, Phenotype details and references, Interaction details and references, Expression Summary, and Protein Info. The Wiki tab points to the locus-specific pages in the SGD Wiki. We invite researchers to edit the wiki pages for their favorite gene(s).
==New Gene Ontology (GO) Evidence Codes==
In order to better distinguish the methods used for sequence-based annotation, the [http://www.geneontology.org Gene Ontology Consortium (GOC)] has created three new evidence designations: Inferred from Sequence Alignment (ISA), Inferred from Sequence Orthology (ISO), and Inferred from Sequence Model (ISM). [http://www.geneontology.org/GO.evidence.shtml Full documentation] on these evidence codes is available at the GOC website. SGD has started using these new subcodes to annotate S. cerevisiae gene products as of April 16th, and these evidence codes are included on the Locus Summary pages, the GO Annotation details and references pages, the downloadable gene_association.sgd file and the GO Term Finder tool.
==Computationally predicted GO annotations added to SGD's gene_association file==
SGD has changed the contents of the GO annotations file. This is a major change as it now includes annotations that are associated with computationally predicted methods. These annotations include computationally predicted annotations to the Gene Ontology created by the Gene Ontology Annotation (GOA) project at EBI, Hinxton UK. The file available from the GO Consortium is called gene_association.sgd.
==Coming Soon: Improved mutant phenotype data==
We have developed a new system for recording detailed information about mutant phenotypes, along with new displays and search tools. Over the past months, we have used this system to curate mutant phenotype data for nearly 5,900 genes, including more than 95% of all Verified ORFs in SGD. We will be providing this new system to SGD users in the near future.
==Summary Paragraphs Progress, 68 new since February 2008==
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 2008 - April 2008), new summary paragraphs for the following 68 features have been added to their respective Locus Summary pages:

:::::::<br>'''List of Summary Paragraphs Added During the Last Quarter'''<br \>
{| class="wikitable"
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005446 ADH1/YOL086C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000004918 ADH2/YMR303C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000004688 ADH3/YMR083W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003225 ADH4/YGL256W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000000349 ADH5/YBR145W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005009 AQR1/YNL065W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003148 ATG1/YGL180W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003965 ATG10/YLL042C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000006253 ATG11/YPR049C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000000421 ATG12/YBR217W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000006389 ATG13/YPR185W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000000332 ATG14/YBR128C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000000664 ATG15/YCR068W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000004769 ATG16/YMR159C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000004415 ATG17/YLR423C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000001917 ATG18/YFR021W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005442 ATG19/YOL082W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005186 ATG2/YNL242W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000002271 ATG20/YDL113C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000006021 ATG21/YPL100W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000000543 ATG22/YCL038C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000004423 ATG23/YLR431C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003714 ATG27/YJL178C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000006087 ATG29/YPL166W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005290 ATG3/YNR007C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005167 ATG4/YNL223W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000006070 ATG5/YPL149W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000001214 ATG7/YHR171W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000000174 ATG8/YBL078C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000002308 ATG9/YDL149W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003786 BNA1/YJR025C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003839 BNA2/YJR078W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000000194 BNA4/YBL098W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000004221 BNA5/YLR231C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000001943 BNA6/YFR047C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000002836 BNA7/YDR428C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000002429 CIS1/YDR022C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000004421 CRN1/YLR429W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000000384 DTR1/YBR180W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000000212 FLR1/YBR008C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003045 HNM1/YGL077C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005338 HOL1/YNR055C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005373 HRD1/YOL013C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000001876 LPD1/YFL018C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000004320 NMA1/YLR328W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003242 NMA2/YGR010W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005735 NPT1/YOR209C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005073 NRK1/YNL129W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005952 PHO85/YPL031C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003005 PNC1/YGL037C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000004199 PNP1/YLR209C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000001382 QDR1/YIL120W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000001383 QDR2/YIL121W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000000247 QDR3/YBR043C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000001116 QNS1/YHR074W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000002327 SFA1/YDL168W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000002200 SIR2/YDL042C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003573 SNX4/YJL036W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000001292 SSM4/YIL030C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000002818 STE14/YDR410C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003951 TPO1/YLL028W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000003370 TPO2/YGR138C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000006360 TPO3/YPR156C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000005799 TPO4/YOR273C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000002369 UGA4/YDL210W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000002808 URH1/YDR400W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000006041 VPS30/YPL120W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000001090 YHK8/YHR048W] || ||  ||  || 
|}

==Two sequence/annotation changes made to the systematic sequence of ''S. cerevisiae''==
As new data become available, SGD curators update the systematic genomic sequence, its gene models, and their annotation. Information regarding sequence and annotation changes can be found via the [http://db.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 2008 - April 2008), the sequence of Chromosome I was updated, affecting [http://db.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000000042 GCV3/YAL044C]; and the annotation of the LTR [http://db.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000007429 YCRCtau1] on Chromosome III was updated.
==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

*Gene Transcription in Yeast
:Sant Feliu de Guixols, Spain
:June 21-26, 2008

*Yeast Chromosome Structure, Replication and Segregation
:Carefree Resort, Carefree, AZ 
:June 22 - June 27, 2008

*Cellular & Molecular Fungal Biology
:Holderness School, Plymouth, NH 
:June 29 - July 4, 2008

*Yeast Genetics and Molecular Biology Meeting
:University of Toronto, Toronto, Ontario, Canada
:July 22-27, 2008

*Plant & Fungal Cytoskeleton
:Il Ciocco, Lucca (Barga), Italy 
:August 3 - 8, 2008

*12th International Congress on Yeasts
:Kyiv Aviation University, Kyiv (Kiev), Ukraine 
:August 11 - August 15, 2008

*Small Meeting on Yeast Transport and Energetics
:Bom Jesus, Braga, Portugal
:September 6-9, 2008

*EMBO Workshop on Evolutionary and Environmental Genomics of Yeasts
:EMBL Heidelberg, Germany 
:October 1 - 5, 2008
<br>asterisks indicate attendance by SGD.*<br \>
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