Nucleic Acids Research Advance Access originally published online on November 16, 2006
Nucleic Acids Research 2007 35(Database issue):D468-D471; doi:10.1093/nar/gkl931
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Nucleic Acids Research, 2007, Vol. 35, Database issue D468-D471
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
Expanded protein information at SGD: new pages and proteome browser
Department of Genetics, School of Medicine, Stanford University Stanford, CA 94305-5120, USA 1 Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University Washington Road, Princeton, NJ 08544, USA
*To whom correspondence should be addressed. Tel: +1 650 723 7541; Fax: +1 650 725 1534; Email: cherry{at}stanford.edu
Received September 14, 2006. Revised October 12, 2006. Accepted October 12, 2006.
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.
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