The Saccharomyces Genome Database Variant Viewer

Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer.

Figure 1.

Pipeline of Variant Viewer data. The pipeline of variant data begins by fetching sequences for the reference strain and 11 alternative strains. The sequences for each feature are aligned using Clustal Omega (7) and stored in SGD's database. The alignment data is then combined with GO annotations, protein domains, introns for the reference genome and location in the reference genome to a JSON object that is indexed into Elasticsearch. When a user visits the site, the SGD server responds with the same JSON object, which the browser can use to render the interface.

Figure 2.

Matrix visualization of alignments. (A) A matrix is provided showing the available strains with a dendrogram illustrating their sequence relationships. The rows represent the ORFs and their variation relative to the reference. The table allows users to scroll through visible features. (B) The matrix is colored with a scale that corresponds to their alignment to S288C (C) User is allowed to toggle between DNA or protein variation view. (D) A search bar allows users to limit the features that appear in the display.

Figure 3.

ORF view. The lollipop variant visualization highlights variation within a single ORF. In this example the ECM33 ORF nucleotide variation between 11 strain sequences is shown. SNPs, insertions and deletions are represented as symbols called lollipops. Below the lollipop visualization, the varied segments of the aligned sequences are shown. Mousing over a lollipop in the upper portion of the display highlights the corresponding sequence across the visible strains. In this view, users can also toggle between DNA and protein modes.