Kyla at 22:42, 19 December 2013

2013-12-19T22:42:57Z

Kyla at 22:39, 19 December 2013

2013-12-19T22:39:24Z

Kyla: Created page with "Category: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 fo..."

2013-12-19T17:10:10Z

Created page with "Category: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 fo..."

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[[Category: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.

 '''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. 
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← Older revision		Revision as of 22:39, 19 December 2013
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	[[Category:Newsletter]]		[[Category:Newsletter]]
		+	<br>'''About this newsletter:'''<br \>
	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.		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.

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 [[Category:Newsletter]]
 <br>'''About this newsletter:'''<br \>
-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.
+<br>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.<br \>
 As always, please contact SGD with any comments or suggestions at: yeast-curator@genome.stanford.edu

SGD Quarterly Newsletter, Fall 2003 - Revision history

Kyla at 22:42, 19 December 2013

Kyla at 22:39, 19 December 2013

Kyla: Created page with "Category: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 fo..."