YSB: Yeast SNPs Browser

Nucleotide-level variation across Saccharomyces cerevisiae strains.

The Yeast SNPs Browser has been retired.

Complete data from publications are still available on our FTP site and SGD. Dumps of the mysql databases are also available here. Data from both publications are accurate to the December 2008 version of the yeast genome, as provided by SGD.

YSB displayed data described in two different publications:

  1. Schacherer and Shapiro et al (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae Nature Feb 11 [Epub ahead of print].

    Polymorphisms from this paper were viewed by showing SNPs as tick marks, with deletions having width indicating their extent. The SNPs shown in this view were grouped across strains, and only those SNPs which occurred in at least two strains were included.

    All potential SNPs and deletions could also be shown, along with the uncertainty in their position. Each peak was a region in which SNPscanner values were positive, and would extend for many base pairs around the location of the final call of the SNP. This track included all potential SNPs, some of which may not have been present in the grouped set.

    One could download a file containing the SNPs for one's current region. This would include grouped SNP calls for all strains (including unselected strains). More detailed information for each call could also be downloaded as a GFF file.

  2. Schacherer et al. (2007) Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. PLoS ONE 2(3): e322.

    Data from this publication could be viewed in two ways: by viewing the predicted SNPs in particular strains by choosing strains of interest, or by viewing the SNP scores over significant regions of the chromosome.

Note that with the technique used in both of these methods, the actual sequence of the predicted SNPs in the other yeast strains is not determined; only the location of the SNP is predicted. See the papers for more information.

For the source code for this browser, see the Generic Model Organism Database Project.
Thanks to Lincoln Stein, Josh Stein, and Scott Cain for help with configuring this implementation of Gbrowse.
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Generic genome browser version 1.66