September 15, 2011
SGD has upgraded Yeast Biochemical Pathways (YeastCyc) to Pathway Tools Version 15.0. This version gives the pathway database a new look and offers new features for querying and analyzing data. A pathway-specific toolbar, available on each pathway web page, provides easy navigation and new features, including options to highlight pathways and substrates on the cellular overview and to download a list of genes from a specific pathway. Pathway files (yeastcyc15_201109.tar.gz and biochemical_pathways.tab) can be downloaded from SGD’s downloads page.
Categories: Website changes
September 06, 2011
SGD has updated both its BLAST Search and Pattern Matching (PatMatch) tools to include genomic, coding, and protein sequences from 26 additional S. cerevisiae strains. Look for more updates and tools from SGD for analyses of the S. cerevisiae strain genomes in the coming months.
Categories: Sequence, Website changes
September 01, 2011
SGD has updated its file Downloads Site. The new look includes complete genomic and protein sequence files for the current S288C reference sequence (Release 64) and all previous releases. Genomic sequence and annotation for numerous S. cerevisiae strains are also available for download. As always we make available many other published datasets and a large collection of information curated by SGD from the literature.
Categories: Website changes
August 22, 2011
SGD’s “Advanced Search” and “Batch Download” tools will be retired on August 31st. All of the functions of these tools, plus many more, can be accomplished by YeastMine, which offers flexible queries and fast retrieval of multiple datatypes from SGD for a custom list of genes or proteins.
Short video tutorials that walk you through some of the basic actions in YeastMine are also available.
Categories: Website changes
February 23, 2011
Expression analysis at SGD has a new powerful interface and many new datasets. The new interface uses a tool called SPELL (Serial Pattern of Expression Levels Locator). This analysis tool facilitates the rapid identification of the most informative datasets and co-expressed genes based on patterns of expression shared with the query gene(s). By transitioning to this tool, expression data from a comprehensive collection of almost 400 datasets are now available at SGD. The expression analysis tool can be accessed via the expression tab, the expression summary histogram, and in the functional analysis pulldown located on Locus Summary pages. These new data and the SPELL interface have been provided through a collaboration with the SGD Colony at Princeton University. Thanks to Peter Koppstein, Lance Parsons, and Kara Dolinski for help with data preparation and implementation of SPELL at SGD. SPELL was developed by the Troyanskaya lab at Princeton University (Hibbs et al. (2007) Bioinformatics 23:2692).
Categories: Data updates, Website changes
February 15, 2011
SGD’s Batch Download tool will be retired soon, because all of its functions and many more can now be accomplished via YeastMine, which offers flexible queries and fast retrieval of multiple datatypes from SGD for a custom list of genes or proteins. Please contact us if you have any concerns.
Categories: Website changes
February 15, 2011
YeastMine, a powerful data search and retrieval tool, has been upgraded to InterMine version 0.95. This software update includes many new features, improvements and bug fixes. Key new features include a completely redesigned homepage, a more powerful multifaceted keyword search and template ranking by frequency of search. YeastMine queries multiple datatypes: chromosomal features, protein features, GO annotations, phenotypes, interaction data and curated literature. YeastMine will soon replace several search tools at SGD. Please explore its powerful query options and send us feedback.
YeastMine was created through an NIH funded collaboration between InterMine, the Rat Genome Database (RGD), and the Zebrafish Model Organism Database (ZFIN) to provide interoperability between model organism databases.
Categories: Website changes