New & Noteworthy

Textpresso now includes publications from 2011

June 21, 2011

The SGD full-text literature search (powered by Textpresso) has been upgraded and updated to include 58,000 papers. Textpresso now includes the ability to restrict your searches to a subset of PMIDs as well as limit the results to a specific section of a paper. The full-text literature search can be accessed via the Full-text Search link on the home page. Thanks to Arun Rangarajan and Hans-Michael Muller from Wormbase for their help upgrading the software.

Categories: Data updates

New Genome-wide High-throughput Data Tracks Added to GBrowse and PBrowse

June 09, 2011

We’ve added new data tracks to our GBrowse genome viewer from eight publications, including recent surveys of nucleosome occupancy and positioning (Kaplan et al., 2009; Field et al., 2008; Mavrich et al., 2008; Lee et al., 2007); ncRNAs and RNA secondary structures (Lardenois et al., 2011 and Kertesz et al., 2010); and transcription factor and RNA Pol II occupancy (Venters et al., 2011 and Mayer et al., 2010). We have also added a data track to our Pbrowse proteome browser, displaying mature N-termini of mitochondrial proteins as determined by Vögtle et al., 2009. Both GBrowse and PBrowse have been upgraded to the most recent software with several new features.
We invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers pre- and/or post-publication as we move forward. Watch for the regular addition of new tracks to SGD’s GBrowse and PBrowse in the future! Please contact us if you are interested in participating or have questions and comments.

Categories: New Data, Data updates

New Expression Analysis Tool and Datasets

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