Expanded protein information at SGD: new pages and proteome browser

Abstract

The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available protein information and has prompted the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) to enhance the depth and accessibility of protein annotations. In particular, we have expanded ongoing efforts to improve the integration of experimental information and sequence-based predictions and have redesigned the protein information web pages. A key feature of this redesign is the development of a GBrowse-derived interactive Proteome Browser customized to improve the visualization of sequence-based protein information. This Proteome Browser has enabled SGD to unify the display of hidden Markov model (HMM) domains, protein family HMMs, motifs, transmembrane regions, signal peptides, hydropathy plots and profile hits using several popular prediction algorithms. In addition, a physico-chemical properties page has been introduced to provide easy access to basic protein information. Improvements to the layout of the Protein Information page and integration of the Proteome Browser will facilitate the ongoing expansion of sequence-specific experimental information captured in SGD, including post-translational modifications and other user-defined annotations. Finally, SGD continues to improve upon the availability of genetic and physical interaction data in an ongoing collaboration with BioGRID by providing direct access to more than 82,000 manually-curated interactions.

Figure 1

The SGD Proteome Browser. The Pdr5p primary protein sequence is shown in the SGD Proteome Browser, a GBrowse-derived tool used to display predicted features, including: InterProScan-derived domains and motifs color-coded by HMM type, hidden Markov model-derived transmembrane domains (TMHMM), the Kyte-Doolittle hydropathy plot and profile hits. The Proteome Browser can also be used for the display of experimentally-derived features. HMM Domains are color-coded by originating resource: orange/yellows = Pfam, reds = Superfamily, purples = Gene3D, greens = Panther, blues = TIGRFAM and browns = SMART.