Kyla at 22:36, 19 December 2013

2013-12-19T22:36:15Z

Kyla: Created page with "Category:Newsletter
'''SGD Newsletter, February 2006'''

'''About this newsletter:'''

This is the February 2006 issue of the quarterly SGD ..."

2013-12-19T19:50:19Z

Created page with "Category:Newsletter <big>'''SGD Newsletter, February 2006'''</big> '''About this newsletter:''' This is the February 2006 issue of the quarterly SGD ..."

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[[Category:Newsletter]]
 <big>'''SGD Newsletter, February 2006'''</big> 
 '''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. 

==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.
{| class="wikitable"
|-
! Chromosome !! Sequence/Annotation Changes !! New Features Added
|-
| I || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000000081 SWH1/YAR042W] || None
|-
| II || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ybr286w APE3/YBR286W] || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ybr056c-b YBR056C-B], [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ybr201c-a YBR201C-A], [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snr161 SNR161/snR161]
|-
| III || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YCL048W-A YCL048W-A], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000000530 AGP1/YCL025C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000028518 ADF1/YCL058W-A] || None
|-
| IV || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR461C-A YDR461C-A], [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR374W-A YDR374W-A], [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR119W-A YDR119W-A], [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDL007C-A YDL007C-A], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ydl208w NHP2/YDL208W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ydr378c LSM6/YDR378C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000002490 RRP8/YDR083W] || None
|-
| V || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yer030w CHZ1/YER030W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yer050c RSM18/YER050C] || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snr80 SNR80/snR80]
|-
| VI || None || None
|-
| VII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ygr236c SPG1/YGR236C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ygr225w AMA1/YGR225W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ygr226c YGR226C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000003320 CTT1/YGR088W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ygl194c-a YGL194C-A]
|-
| VIII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000001957 SAE3/YHR079C-A], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yhr163w SOL3/YHR163W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yhl026c YHL026C] || None
|-
| IX || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yil076w SEC28/YIL076W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000001315 GPP1/YIL053W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000001305 CBR1/YIL043C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=yil102c-a YIL102C-A]
|-
| X || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yjl046w AIM22/YJL046W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000003698 JJJ2/YJL162C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000003706 ASG7/YJL170C] || None
|-
| XI || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000001750 UTH1/YKR042W], [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YKL023C-A YKL023C-A], [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YKL065W-A YKL065W-A], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ykr058w GLG1/YKR058W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YKL039W PTM1/YKL039W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YKL099C UTP11/YKL099C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YKL137W CMC1/YKL137W] || None
|-
| XII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YLR146W-A YLR146W-A], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YLR329W REC102/YLR329W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000004393 DUS3/YLR401C] || None
|-
| XIII || None || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000081376 snR85], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000114171 RNA170]
|-
| XIV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000005243 TRF5/YNL299W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ynl304w YPT11/YNL304W] || None
|-
| XV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yor074c CDC21/YOR074C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yor091w TMA46/YOR091W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yor147w MDM32/YOR147W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yor221c MCT1/YOR221C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=yor330c MIP1/YOR330C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000005778 TMA16/YOR252W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000005512 FRE7/YOL152W] || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000081375 snR81]
|-
| XVI || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=ypr169w JIP5/YPR169W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YPL052W OAZ1/YPL052W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000113724 YPL052W-A] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ypr145c-a YPR145C-A]
|-
| Mito || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000007263 AI3/Q0060], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000007264 AI4/Q0065] || None
|}
==SGD Publication Describes the Genome Snapshot Resource in the 2006 NAR Database Issue==
The 2006 Nucleic Acids Research [http://nar.oxfordjournals.org/content/34/suppl_1.toc Database issue] features a paper ([http://nar.oxfordjournals.org/content/34/suppl_1/D442.full 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'' ([http://www.candidagenome.org CGD]) and ''Schizosaccharomyces pombe'' ([http://www.pombase.org ''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 [http://wolfe.ucd.ie 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 [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000113653 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''' 
{| class="wikitable"
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ADE2 ADE2/YOR128C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ADH1 ADH1/YOL086C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ADH2 ADH2/YMR303C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ADH3 ADH3/YMR083W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ADH4 ADH4/YGL256W] || ADH5/YBR145W
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ADR1 ADR1/YDR216W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=AVO1 AVO1/YOL078W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=AVO2 AVO2/YMR068W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=BIT61 BIT61/YJL058C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=CDD1 CDD1/YLR245C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=FCY1 FCY1/YPR062W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=FCY2 FCY2/YER056C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=FUI1 FUI1/YBL042C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=FUR1 FUR1/YHR128W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=FUR4 FUR4/YBR021W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GLC7#summaryparagraph GLC7/YER133W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GND1 GND1/YHR183W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GND2 GND2/YGR256W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=HO HO/YDL227C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=KOG1 KOG1/YHR186C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LSM1 LSM1/YJL124C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LSM2 LSM2/YBL026W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LSM3 LSM3/YLR438C-A]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LSM4 LSM4/YER112W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LSM5 LSM5/YER146W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LSM6 LSM6/YDR378C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LSM7 LSM7/YNL147W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LSM8 LSM8/YJR022W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LST8#summaryparagraph LST8/YNL006W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=MAK31 MAK31/YCR020C-A] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=PSF1 PSF1/YDR013W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=PSF2 PSF2/YJL072C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=PSF3 PSF3/YOL146W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RBK1 RBK1/YCR036W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RKI1 RKI1/YOR095C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RPE1 RPE1/YJL121C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SFA1 SFA1/YDL168W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SLD5 SLD5/YDR489W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SLM1 SLM1/YIL105C] || SLM2/YNL047C || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SMB1 SMB1/YER029C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SMD1 SMD1/YGR074W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SMD2 SMD2/YLR275W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SMD3 SMD3/YLR147C] || SME1/YOR159C || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SMX2 SMX2/YFL017W-A] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SMX3 SMX3/YPR182W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SNX3 SNX3/YOR357C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SOL1 SOL1/YNR034W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SOL2 SOL2/YCR073W-A] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SOL3 SOL3/YHR163W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SOL4 SOL4/YGR248W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SPT15 SPT15/YER148W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=TAL1 TAL1/YLR354C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=TCO89 TCO89/YPL180W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=TKL1 TKL1/YPR074C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=TKL2 TKL2/YBR117C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=TSC11 TSC11/YER093C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=URA1 URA1/YKL216W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=URA10 URA10/YMR271C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=URA2 URA2/YJL130C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=URA3 URA3/YEL021W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=URA4 URA4/YLR420W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=URA5 URA5/YML106W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=URA7 URA7/YBL039C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=URA8 URA8/YJR103W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=URH1 URH1/YDR400W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=URK1 URK1/YNR012W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YJL068C YJL068C] || ||
|}

==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.* 
 '''Manage your subscription''' 
 To SUBSCRIBE: If you think friends or colleagues would be interested in receiving this newsletter, they can subscribe by filling out an [http://www.yeastgenome.org/cgi-bin/colleague/colleagueSearch SGD colleague form], and selecting 'Y' to receive the SGD newsletter. 
 '''[http://www.yeastgenome.org/cgi-bin/suggestion CONTACT SGD]'''

@@ Line 1: / Line 1: @@
 [[Category:Newsletter]]
 <br>'''About this newsletter:'''<br \>
 <br>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.<br \>

SGD Quarterly Newsletter, Winter 2006 - Revision history

Kyla at 22:36, 19 December 2013

Kyla: Created page with "Category:Newsletter '''SGD Newsletter, February 2006''' '''About this newsletter:''' This is the February 2006 issue of the quarterly SGD ..."

Kyla: Created page with "Category:Newsletter
'''SGD Newsletter, February 2006'''

'''About this newsletter:'''

This is the February 2006 issue of the quarterly SGD ..."